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This '''list of RNA structure prediction software''' is a compilation of software tools and web portals used for [[RNA structure]] prediction.
I am 26 years old and my name is Leora Ruddell. I life in Lindental (Switzerland).<br><br>My webpage: [http://dmoproz.com/Activity-Feed/My-Profile/UserId/62988 wordpress dropbox backup]
 
==Single sequence secondary structure prediction==
{| class="wikitable sortable"
! Name
! Description
! Knots<br/><ref group=Note>'''Knots:''' [[Pseudoknot]] prediction, <yes|no>.</ref>
! Links || References
|-
! [[CentroidFold]]
|Secondary structure prediction based on generalized centroid estimator || no || [http://www.ncrna.org/centroidfold/ sourcecode] [http://www.ncrna.org/centroidfold/ webserver]||<ref name="pmid19095700">{{cite journal | author = Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai | title = Predictions of RNA secondary structure using generalized centroid estimators | journal = Bioinformatics | volume = 25 | issue = 4 | pages = 465–473 | year = 2009 | pmid = 19095700 | doi = 10.1093/bioinformatics/btn601  }}</ref>
|-
! [[CentroidHomfold]]
|Secondary structure prediction by using homologous sequence information || no || [http://www.ncrna.org/centroidfold/ sourcecode] [http://www.ncrna.org/centroidhomfold/ webserver] ||<ref name="pmid19478007">{{cite journal | author = Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai | title = Predictions of RNA secondary structure by combining homologous sequence information | journal = Bioinformatics | volume = 25 | issue = 12 | pages = i330 - i3388 | year = 2009 | pmid = 19478007 | doi = 10.1093/bioinformatics/btp228  }}</ref>
|-
! [[Context Fold]]
|An RNA secondary structure prediction software based on feature-rich trained scoring models. || no || [http://www.cs.bgu.ac.il/~negevcb/contextfold/ContextFold_1_00.zip sourcecode] [http://www.cs.bgu.ac.il/~negevcb/contextfold/ webserver] ||<ref name="pmid22035327">{{cite journal | author = Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson | title = Rich parameterization improves RNA structure prediction | journal = Journal of Computational Biology | volume = 18 | issue = 11 | pages = 1525–1542 | year = 2011 | pmid = 22035327 | doi = 10.1089/cmb.2011.0184  }}</ref>
|-
! [[CONTRAfold]]
|Secondary structure prediction method based on conditional log-linear models (CLLMs), a flexible class of probabilistic models which generalize upon [[SCFG]]s by using discriminative training and [[feature-rich]] scoring. || no || [http://contra.stanford.edu/contrafold/ sourcecode] [http://contra.stanford.edu/contrafold/server.html webserver]||<ref name="pmid16873527">{{cite journal | author = Do CB, Woods DA, Batzoglou S | title = CONTRAfold: RNA secondary structure prediction without physics-based models | journal = Bioinformatics | volume = 22 | issue = 14 | pages = e90–8 | year = 2006 | pmid = 16873527 | doi = 10.1093/bioinformatics/btl246 }}</ref>
|-
! [[CyloFold]]
|Secondary structure prediction method based on placement of helices allowing complex pseudoknots. || yes || [http://cylofold.abcc.ncifcrf.gov/ webserver] ||<ref name="pmid20501603">{{cite journal | author = Bindewald E, Kluth T, Shapiro BA | title = CyloFold: secondary structure prediction including pseudoknots | journal = Nucleic Acids Research | volume = Suppl | issue = W | pages = 368–72 | year = 2010 | pmid = 20501603 | pmc = 2896150 | doi = 10.1093/nar/gkq432 }}</ref>
|-
! [[IPknot]]
|Fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. || yes || [https://code.google.com/p/ipknot/ sourcecode] [http://rna.naist.jp/ipknot/ webserver] ||<ref name="pmid21685106">{{cite journal | author = Sato K, Kato Y, Hamada M, Akutsu T, Asai K | title = IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming | journal = Bioinformatics | volume = 27 | issue = 13 | pages = i85-93 | year = 2011 | pmid = 21685106 | pmc = 3117384  | doi = 10.1093/bioinformatics/btr215 }}</ref>
|-
! [[KineFold]]
|Folding kinetics of RNA sequences including pseudoknots by including an implementation of the partition function for knots.||yes||[http://kinefold.curie.fr/ linuxbinary,] [http://kinefold.curie.fr/cgi-bin/form.pl webserver]||<ref name="pmid15980546">{{cite journal | author = Xayaphoummine A, Bucher T, Isambert H | title = Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots | journal = Nucleic Acids Res. | volume = 33 | issue = Web Server issue | pages = W605–10 | year = 2005 | pmid = 15980546 | doi = 10.1093/nar/gki447 | pmc = 1160208 }}</ref><ref name="pmid14676318">{{cite journal | author = Xayaphoummine A, Bucher T, Thalmann F, Isambert H | title = Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 100 | issue = 26 | pages = 15310–5 | year = 2003 | pmid = 14676318 | doi = 10.1073/pnas.2536430100 | pmc = 307563 |arxiv = physics/0309117 |bibcode = 2003PNAS..10015310X }}</ref>
|-
! [[Mfold]]
|[[Gibbs free energy|MFE]] (Minimum Free Energy) RNA structure prediction algorithm. || no || [http://www.bioinfo.rpi.edu/applications/mfold/ sourcecode,] [http://mfold.rit.albany.edu/?q=mfold webserver] || <ref name="pmid6163133">{{cite journal | author = Zuker M, Stiegler P | title = Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information | journal = Nucleic Acids Res. | volume = 9 | issue = 1 | pages = 133–48 | year = 1981 | pmid = 6163133 | doi = 10.1093/nar/9.1.133 | pmc = 326673 }}</ref>
|-
! [[Pknots]]
|A dynamic programming algorithm for optimal RNA pseudoknot prediction using the nearest neighbour energy model. ||yes||[http://selab.janelia.org/software.html sourcecode]||<ref name="pmid9925784">{{cite journal | author = Rivas E, Eddy SR | title = A dynamic programming algorithm for RNA structure prediction including pseudoknots | journal = J. Mol. Biol. | volume = 285 | issue = 5 | pages = 2053–68 | year = 1999 | pmid = 9925784 | doi = 10.1006/jmbi.1998.2436 }}</ref>
|-
! [[PknotsRG]]
|A dynamic programming algorithm for the prediction of a restricted class of RNA pseudoknots.||yes||[http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/welcome.html sourcecode,] [http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/submission.html webserver]||<ref name="pmid17478505">{{cite journal | author = Reeder J, Steffen P, Giegerich R | title = pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows | journal = Nucleic Acids Res. | volume = 35 | issue = Web Server issue | pages = W320–4 | year = 2007 | pmid = 17478505 | doi = 10.1093/nar/gkm258 | pmc = 1933184 }}</ref>
|-
! [[RNA123]]
|Secondary structure prediction via thermodynamic-based folding algorithms and novel structure-based sequence alignment specific for RNA.|| yes || [http://www.rna123.com/ webserver] ||
|-
! [[RNAfold]]
|MFE RNA structure prediction algorithm. Includes an implementation of the partition function for computing basepair probabilities and circular RNA folding.|| no || [http://www.tbi.univie.ac.at/~ivo/RNA/ sourcecode,] [http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi webserver] ||
<ref name="pmid6163133"/><ref name="RNAInverse">{{cite journal | author = I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster | title = Fast Folding and Comparison of RNA Secondary Structures. | journal =  Monatshefte f. Chemie | volume = 125 | issue = 2 | pages = 167–188 | year = 1994 | doi = 10.1007/BF00818163}}</ref><ref name="pmid1695107">{{cite journal | author = McCaskill JS | title = The equilibrium partition function and base pair binding probabilities for RNA secondary structure | journal = Biopolymers | volume = 29 | issue = 6-7 | pages = 1105–19 | year = 1990 | pmid = 1695107 | doi = 10.1002/bip.360290621 }}</ref><ref name="pmid16452114">{{cite journal | author = Hofacker IL, Stadler PF | title = Memory efficient folding algorithms for [[circular RNA]] secondary structures | journal = Bioinformatics | volume = 22 | issue = 10 | pages = 1172–6 | year = 2006 | pmid = 16452114 | doi = 10.1093/bioinformatics/btl023 }}</ref><ref name="pmid17611759">{{cite journal | author = Bompfünewerer AF, Backofen R, Bernhart SH, ''et al.'' | title = Variations on RNA folding and alignment: lessons from Benasque | journal = J Math Biol | volume = 56 | issue = 1-2 | pages = 129–144 | year = 2008 | pmid = 17611759 | doi = 10.1007/s00285-007-0107-5 }}</ref>
|-
! [[RNAshapes]]
|MFE RNA structure prediction based on abstract shapes. Shape abstraction retains adjacency and nesting of structural features, but disregards helix lengths, thus reduces the number of suboptimal solutions without losing significant information. Furthermore, shapes represent classes of structures for which probabilities based on Boltzmann-weighted energies can be computed.|| no || [http://bibiserv.techfak.uni-bielefeld.de/download/tools/rnashapes.html source & binaries,] [http://bibiserv.techfak.uni-bielefeld.de/rnashapes/ webserver] ||<ref name="abstract shapes">{{cite journal | author = R. Giegerich, B.Voß, M. Rehmsmeier | title = Abstract shapes of RNA. | journal = Nucleic Acids Res. | volume = 32 | issue = 16 | pages = 4843–4851 | year = 2004 | doi = 10.1093/nar/gkh779 | pmid = 15371549 | pmc = 519098}}</ref><ref name="shape probabilities">{{cite journal | author = B. Voß, R. Giegerich, M. Rehmsmeier | title = Complete probabilistic analysis of RNA shapes. | journal = BMC Biology | volume = 4 | year = 2006 | doi = 10.1186/1741-7007-4-5 | pmid = 16480488 | pages = 5 | pmc = 1479382}}</ref>
|-
! [[RNAstructure]]
|A program to predict lowest free energy structures and base pair probabilities for RNA or DNA sequences.  Programs are also available to predict Maximum Expected Accuracy structures and these can include pseudoknots.  Structure prediction can be constrained using experimental data, including SHAPE, enzymatic cleavage, and chemical modification accessibility. Graphical user interfaces are available for Windows and for Mac OS-X/Linux.  Programs are also available for use with Unix-style text interfaces.  Additionally, a C++ class library is available.|| yes || [http://rna.urmc.rochester.edu/RNAstructure.html source & binaries]  ||
<ref name="RNAstructure">{{cite journal | doi = 10.1073/pnas.0401799101 | author = D.H. Mathews, M.D. Disney, J. L. Childs, S.J. Schroeder, M. Zuker, D.H. Turner  | title = Incorporating chemical modification constraints into a dynamic programming algorothm for prediction of RNA secondary structure. | journal =  Proceedings of the National Academy of Sciences of the United States of America| volume = 101 | issue = 19 | pages = 7287–7292 | year = 2004 | pmid = 15123812 | pmc = 409911 | bibcode=2004PNAS..101.7287M}}</ref><ref name="RNAstructure-partition">{{cite journal | author = D.H. Mathews  | title = Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. | journal =  RNA | volume = 10 | pages = 1178–1190 | year = 2004 | pmid = 15272118 | issue = 8 | doi = 10.1261/rna.7650904 | pmc = 1370608 }}</ref>
|-
! [[Sfold]]
|Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities. || no ||[http://sfold.wadsworth.org webserver]||<ref name="pmid14654704">{{cite journal | author = Ding Y, Lawrence CE | title = A statistical sampling algorithm for RNA secondary structure prediction | journal = Nucleic Acids Res. | volume = 31 | issue = 24 | pages = 7280–301 | year = 2003 | pmid = 14654704 | doi = 10.1093/nar/gkg938 | pmc = 297010 }}</ref><ref name="pmid15215366">{{cite journal | author = Ding Y, Chan CY, Lawrence CE | title = Sfold web server for statistical folding and rational design of nucleic acids | journal = Nucleic Acids Res. | volume = 32 | issue = Web Server issue | pages = W135–41 | year = 2004 | pmid = 15215366 | doi = 10.1093/nar/gkh449 | pmc = 441587 }}</ref><ref name="pmid16043502">{{cite journal | author = Ding Y, Chan CY, Lawrence CE | title = RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble | journal = RNA | volume = 11 | issue = 8 | pages = 1157–66 | year = 2005 | pmid = 16043502 | doi = 10.1261/rna.2500605 | pmc = 1370799 }}</ref><ref name="pmid16109749">{{cite journal | author = Chan CY, Lawrence CE, Ding Y | title = Structure clustering features on the Sfold Web server | journal = Bioinformatics | volume = 21 | issue = 20 | pages = 3926–8 | year = 2005 | pmid = 16109749 | doi = 10.1093/bioinformatics/bti632 }}</ref>
|-
! [[UNAFold]]
|The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. || no || [http://www.bioinfo.rpi.edu/applications/hybrid/download.php sourcecode] || <ref name="pmid18712296">{{cite journal |author=Markham NR, Zuker M |title=UNAFold: software for nucleic acid folding and hybridization. |journal=Methods Mol Biol |volume=453 |issue= |pages=3–31 |year=2008 |pmid=18712296 |doi=10.1007/978-1-60327-429-6_1}}</ref>
|-
! [[Crumple]]
|Crumple is simple, cleanly written software for producing the full set of possible secondary structures for a single sequence, given optional constraints. || no || [http://adenosine.chem.ou.edu#crumple sourcecode] || <ref name="pmid21723827">{{cite journal |author=Schroeder S, Bleckley S, Stone JW |title=Ensemble of secondary structures for encapsidated satellite tobacco mosaic virus RNA consistent with chemical probing and crystallography constraints. |journal=Biophysical Journal |volume=101 |issue=1 |pages=167–175 |year=2011 |pmid=21723827 |doi=10.1016/j.bpj.2011.05.053|bibcode = 2011BpJ...101..167S }}</ref>
|-
! [[Sliding Windows & Assembly]]
|Sliding windows and assembly is a tool chain for folding long series of similar hairpins. || no || [http://adenosine.chem.ou.edu#sliding sourcecode] || <ref name="pmid21723827"/>
|-
| colspan=5|
;Notes:{{reflist|group=Note}}
|}
 
==Single sequence tertiary structure prediction==
{| class="wikitable sortable"
! Name
! Description
! Knots<br/><ref group=Note>'''Knots:''' [[Pseudoknot]] prediction, <yes|no>.</ref>
! Links || References
|-
! [[BARNACLE]]
|A Python library for the probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA-like on a local length scale. || yes || [http://sourceforge.net/projects/barnacle-rna/ sourcecode] || <ref name="pmid19543381">{{cite journal |author=Frellsen J, Moltke I, Thiim M, Mardia KV, Ferkinghoff-Borg J, Hamelryck T |editor1-last=Gardner |editor1-first=Paul |title=A probabilistic model of RNA conformational space. |journal=PLoS Comput Biol |volume=5 |issue=6 |pages=e1000406 |year=2009 |pmid=19543381 |doi=10.1371/journal.pcbi.1000406 |pmc=2691987}}</ref>
|-
! [[FARNA]]
|Automated de novo prediction of native-like RNA tertiary structures . || yes || [http://faculty.washington.edu/rhiju/FARNA/ sourcecode] || <ref name="pmid17726102">{{cite journal |author=Das R, Baker D |title=Automated de novo prediction of native-like RNA tertiary structures |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=104 |issue=37 |pages=14664–9 |date=September 2007 |pmid=17726102 |pmc=1955458 |doi=10.1073/pnas.0703836104 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=17726102|bibcode = 2007PNAS..10414664D }}</ref>
|-
! [[iFoldRNA]]
|three-dimensional RNA structure prediction and folding || yes || [http://iFoldRNA.dokhlab.org webserver] || <ref name="pmid18579566">{{cite journal |author=Sharma S, Ding F, Dokholyan NV |title=iFoldRNA: three-dimensional RNA structure prediction and folding |journal=Bioinformatics |volume=24 |issue=17 |pages=1951–2 |date=September 2008 |pmid=18579566 |pmc=2559968 |doi=10.1093/bioinformatics/btn328 |url=http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=18579566}}</ref>
|-
! [[MC-Fold MC-Sym Pipeline]]
| Thermodynamics and Nucleotide cyclic motifs for RNA structure prediction algorithm. 2D and 3D structures. || yes || [http://www.major.iric.ca/MajorLabEn/MC-Tools.html sourcecode,] [http://www.major.iric.ca/MC-Pipeline/ webserver] || <ref name="pmid18322526">{{cite journal | author = Parisien M, Major F | title = The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data | journal = Nature | volume = 452 | issue = 1 | pages = 51–55 | year = 2008 | pmid = 18322526 | doi = 10.1038/nature06684 |bibcode = 2008Natur.452...51P }}</ref>
|-
! [[NAST (software)|NAST]]
|Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters || ? || [https://simtk.org/home/nast executables] || <ref name="pmid20651028">{{cite journal |author=SC Flores, RB Altman |title=Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters |journal=RNA |volume=15 |issue=9 |pages=1769–1778 |date=September 2010 |pmid=20651028 |pmc=2648710 |doi=10.1261/rna.1270809 |url=http://rnajournal.cshlp.org/cgi/pmidlookup?view=long&pmid=19144906}}</ref>
|-
! [[MMB (software)|MMB]]
|Turning limited experimental information into 3D models of RNA || ? || [https://simtk.org/home/rnatoolbox sourcecode] || <ref name="pmid19144906">{{cite journal |author=Jonikas MA, Radmer RJ, Laederach A, ''et al.'' |title=Turning limited experimental information into 3D models of RNA  |journal=RNA |volume=16 |issue=2 |pages=189–99 |date=February 2009 |pmid=19144906 |pmc= 2924536 |doi=10.1261/rna.2112110 |url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924536/}}</ref>
|-
! [[RNA123]]
|An integrated platform for de novo and homology modeling of RNA 3D structures, where coordinate file input, sequence editing, sequence alignment, structure prediction and analysis features are all accessed from a single intuitive graphical user interface. || yes || [http://www.rna123.com/ webserver] ||
|-
! [[RNAComposer]]
|Fully automated prediction of large RNA 3D structures.  || yes || [http://rnacomposer.cs.put.poznan.pl/ webserver] [http://rnacomposer.ibch.poznan.pl/ webserver] || <ref name="pmid22539264">{{cite journal |author= Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW | title = Automated 3D structure composition for large RNAs | journal = Nucleic Acids Res. | volume = 40 | issue = 14 | pages = 1–12 | year = 2012 | pmid = 22539264  |pmc= 3413140 | doi = 10.1093/nar/gks339 }}</ref>
|-
| colspan=5|
;Notes:{{reflist|group=Note}}
|}
 
==Comparative methods==
The single sequence methods mentioned above have a difficult job detecting a small sample of reasonable secondary structures from a large space of possible structures. A good way to reduce the size of the space is to use evolutionary approaches. Structures that have been conserved by evolution are far more likely to be the functional form. The methods below use this approach.
 
{| class="wikitable sortable"
! Name
! Description
! Number of sequences<br/><ref group=Note>'''Number of sequences:''' <any|num>.</ref>
! Alignment<br/><ref group=Note>'''Alignment:''' predicts an [[sequence alignment|alignment]], <input|yes|no>.</ref>
! Structure<br/><ref group=Note>'''Structure:''' predicts [[RNA structure|structure]], <input|yes|no>.</ref>
! Knots<br/><ref group=Note>'''Knots:''' [[Pseudoknot]] prediction, <yes|no>.</ref>
! Link || References
|-
! [[Carnac (software)|Carnac]]
|Comparative analysis combined with MFE folding.||any||no||yes||no||[http://bioinfo.lifl.fr/RNA/carnac/index.php sourcecode,] [http://bioinfo.lifl.fr/RNA/carnac/carnac.php webserver]||<ref name="pmid12499300">{{cite journal | author = Perriquet O, Touzet H, Dauchet M. | title = Finding the common structure shared by two homologous RNAs. | journal =  Bioinformatics. | year = 2003 | volume = 19| issue = 1 | pages = 108–16 | pmid = 12499300 | doi = 10.1093/bioinformatics/19.1.108 }}</ref><ref name="pmid15215367">{{cite journal | author = Touzet H, Perriquet O. | title = CARNAC: folding families of related RNAs. | series = 32| journal = Nucleic Acids Res. | date = Jul 1, 2004| volume = (Web Server issue)| pages = W142–5.| pmid = 15215367 | issue = Web Server issue | doi = 10.1093/nar/gkh415 | pmc = 441553}}</ref>
|-
! [[CentroidAlifold]]
|Common secondary structure prediction based on generalized centroid estimator ||any||no||yes||no|| [http://www.ncrna.org/centroidfold/ sourcecode] [http://www.ncrna.org/centroidfold/ webserver]||<ref name="pmid20843778">{{cite journal | author = Michiaki Hamada, Kengo Sato, Kiyoshi Asai | title = Improving the accuracy of predicting secondary structure for aligned RNA sequences | journal = Nucleic Acids Res. | volume = 39 | issue = 2 | pages = 393–402 | year = 2011 | pmid = 20843778 | doi = 10.1093/nar/gkq792  }}</ref>
|-
! [[CentroidAlign]]
|Fast and accurate multiple aligner for RNA sequences ||any||yes||no||no|| [http://www.ncrna.org/software/centroidalign sourcecode] ||<ref name="pmid19808876">{{cite journal | author = Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai | title = CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score | journal = Bioinformatics | volume = 25 | issue = 24 | pages = 3236–43 | year = 2009 | pmid = 19808876 | doi = 10.1093/bioinformatics/btp580  }}</ref>
|-
! [[CMfinder]]
|an expectation maximization algorithm using covariance models for motif description. Uses heuristics for effective motif search, and a Bayesian framework for structure prediction combining folding energy and sequence covariation.||<math>3\le seqs \le60</math>||yes||yes||no||[http://bio.cs.washington.edu/yzizhen/CMfinder/ sourcecode,] [http://wingless.cs.washington.edu/htbin-post/unrestricted/CMfinderWeb/CMfinderInput.pl webserver,] [http://bio.cs.washington.edu/yzizhen/CMfinder/ website]|| <ref name="pmid16357030">{{cite journal | author = Yao Z, Weinberg Z, Ruzzo WL | title = CMfinder--a covariance model based RNA motif finding algorithm | journal = Bioinformatics | volume = 22 | issue = 4 | pages = 445–52 | year = 2006 | pmid = 16357030 | doi = 10.1093/bioinformatics/btk008 }}</ref>
|-
! [[CONSAN]]
|implements a pinned Sankoff algorithm for simultaneous pairwise RNA alignment and consensus structure prediction.|| 2 || yes || yes || no || [http://selab.janelia.org/software.html sourcecode] || <ref name="pmid16952317">{{cite journal | author = Dowell RD, Eddy SR | title = Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints | journal = BMC Bioinformatics | volume = 7| pages = 400 | year = 2006 | pmid = 16952317 | doi = 10.1186/1471-2105-7-400 | pmc = 1579236 }}</ref>
|-
! [[DAFS (software)|DAFS]]
|Simultaneous aligning and folding of RNA sequences via dual decomposition.|| any || yes || yes || yes || [https://code.google.com/p/dafs-rna/ sourcecode] || <ref name="pmid23060618">{{cite journal | author = Sato K, Kato Y, Akutsu T, Asai K, Sakakibara Y | title = DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition | journal = Bioinformatics | volume = 28| pages = 3218–24 | year = 2012 | pmid = 23060618 | doi = 10.1093/bioinformatics/bts612 }}</ref>
|-
! [[Dynalign]]
|an algorithm that improves the accuracy of structure prediction by combining free energy minimization and comparative sequence analysis to find a low free energy structure common to two sequences without requiring any sequence identity. || 2 || yes || yes || no || [http://rna.urmc.rochester.edu/dynalign.html sourcecode] || <ref name="pmid11902836">{{cite journal | author = Mathews DH, Turner DH | title = Dynalign: an algorithm for finding the secondary structure common to two RNA sequences | journal = J. Mol. Biol. | volume = 317 | issue = 2 | pages = 191–203 | year = 2002 | pmid = 11902836 | doi = 10.1006/jmbi.2001.5351 }}</ref><ref name="pmid15731207">{{cite journal | author = Mathews DH | title = Predicting a set of minimal free energy RNA secondary structures common to two sequences | journal = Bioinformatics | volume = 21 | issue = 10 | pages = 2246–53 | year = 2005 | pmid = 15731207 | doi = 10.1093/bioinformatics/bti349 }}</ref><ref name="pmid17445273">{{cite journal | author = Harmanci AO, Sharma G, Mathews DH | title = Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign | journal = BMC Bioinformatics | volume = 8| pages = 130 | year = 2007 | pmid = 17445273 | doi = 10.1186/1471-2105-8-130 | pmc = 1868766 }}</ref>
|-
! [[FoldalignM]]
|A multiple RNA structural RNA alignment method, to a large extend based on the PMcomp program.||any||yes||yes||no|| [http://foldalign.ku.dk/software/index.html sourcecode]|| <ref name="pmid17324941">{{cite journal | author = Torarinsson E, Havgaard JH, Gorodkin J | title = Multiple structural alignment and clustering of RNA sequences | journal = Bioinformatics | volume = 23 | issue = 8 | pages = 926–32 | year = 2007 | pmid = 17324941 | doi = 10.1093/bioinformatics/btm049 }}</ref>
|-
! [[FRUUT]]
|A pairwise RNA structural alignment tool based on the comparison of RNA trees. Considers alignments in which the compared trees can be rooted differently (with respect to the standard “external loop” corresponding roots), and/or permuted with respect to branching order.||any||yes||input||no||[http://www.cs.bgu.ac.il/~negevcb/FRUUT/code/FRUUT-2.40.jar sourcecode,] [http://www.cs.bgu.ac.il/~negevcb/FRUUT/ webserver]|| <ref name="978-3-642-33122-0_11">{{cite journal | author = Milo Nimrod, Zakov Shay, Katzenelson Erez, Bachmat Eitan, Dinitz Yefim, Ziv-Ukelson Michal | title = RNA Tree Comparisons via Unrooted Unordered Alignments | journal = Algorithms in Bioinformatics | volume = 7534 | pages = 135–148 | year = 2012 | pmid = | doi = 10.1007/978-3-642-33122-0_11 | issn = }}</ref><ref name="pmid23590940">{{cite journal | author = Milo Nimrod, Zakov Shay, Katzenelson Erez, Bachmat Eitan, Dinitz Yefim, Ziv-Ukelson Michal | title = Unrooted unordered homeomorphic subtree alignment of RNA trees | journal = Algorithms for Molecular Biology | volume = 8 | pages = 13 | year = 2013 | pmid = 23590940 | doi = 10.1186/1748-7188-8-13 | issn = 1748-7188}}</ref>
|-
! [[GraphClust]]
|Fast RNA structural clustering method of local RNA secondary structures. Predicted clusters are refined using LocARNA and CMsearch. Due to the linear time complexity for clustering it is possible to analyse large RNA datasets. ||any||yes||yes||no|| [http://www.bioinf.uni-freiburg.de/Software/GraphClust/ sourcecode]|| <ref name="pmid22689765">{{cite journal | author = Heyne S, Costa F, Rose D, Backofen R | title = GraphClust: alignment-free structural clustering of local RNA secondary structures | journal = Bioinformatics | volume = 28 | issue = 12 | pages = i224-i232 | year = 2012 | pmid = 22689765 | doi = 10.1093/bioinformatics/bts224 }}</ref>
|-
! [[KNetFold]]
|Computes a consensus RNA secondary structure from an RNA sequence alignment based on machine learning.||any||input||yes||yes||[http://www-lmmb.ncifcrf.gov/~bshapiro/downloader_v1/register.php linuxbinary,] [http://knetfold.abcc.ncifcrf.gov/ webserver]|| <ref name="pmid16495232">{{cite journal | author = Bindewald E, Shapiro BA | title = RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers | journal = RNA | volume = 12 | issue = 3 | pages = 342–52 | year = 2006 | pmid = 16495232 | doi = 10.1261/rna.2164906 | pmc = 1383574 }}</ref>
|-
! [[LARA (software)|LARA]]
|Produce a global fold and alignment of ncRNA families using integer linear programming and Lagrangian relaxation.||any||yes||yes||no||[https://www.mi.fu-berlin.de/w/LiSA/ sourcecode] || <ref name="pmid17662141">{{cite journal | author = Bauer M, Klau GW, Reinert K. | title = Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.  | journal = BMC Bioinformatics. | volume = 8 | year = 2007 | pmid = 17662141 | doi = 10.1186/1471-2105-8-271 | pages = 271 | pmc = 1955456 }}</ref>
|-
! [[LocaRNA]]
|LocaRNA is the successor of PMcomp with an improved time complexity. It is a variant of Sankoff's algorithm for simultaneous folding and alignment, which takes as input pre-computed base pair probability matrices from McCaskill's algorithm as produced by RNAfold -p. Thus the method can also be viewed as way to compare base pair probability matrices. || any || yes || yes || no || [http://www.bioinf.uni-freiburg.de/Software/LocARNA/ sourcecode,] [http://rna.informatik.uni-freiburg.de:8080/LocARNA/ webserver] || <ref name="pmid17432929">{{cite journal | author = Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R | title = Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. | journal = PLoS Comput Biol. | volume = 3 | issue = 4 | pages = e65 | year = 2007 | pmid = 17432929 | doi = 10.1371/journal.pcbi.0030065 | pmc = 1851984 |bibcode = 2007PLSCB...3...65W }}</ref>
|-
! [[MASTR]]
|A sampling approach using Markov chain Monte Carlo in a [[simulated annealing]] framework, where both structure and alignment is optimized by making small local changes. The score combines the log-likelihood of the alignment, a covariation term and the basepair probabilities.||any||yes||yes||no|| [http://mastr.binf.ku.dk/ sourcecode]|| <ref name="pmid17038338">{{cite journal | author = Lindgreen S, Gardner PP, Krogh A | title = Measuring covariation in RNA alignments: physical realism improves information measures | journal = Bioinformatics | volume = 22 | issue = 24 | pages = 2988–95 | year = 2006 | pmid = 17038338 | doi = 10.1093/bioinformatics/btl514 }}</ref><ref name="pmid18006551">{{cite journal | author = Lindgreen S, Gardner PP, Krogh A | title = MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing | journal = Bioinformatics | volume = 23 | issue = 24 | pages = 3304–11 | year = 2007 | pmid = 18006551 | doi = 10.1093/bioinformatics/btm525 }}</ref>
|-
! [[Multilign]]
|This method uses multiple Dynalign calculations to find a low free energy structure common to any number of sequences. It does not require any sequence identity. || any || yes || yes || no || [http://rna.urmc.rochester.edu/RNAstructure.html sourcecode] || <ref name="pmid21193521">{{cite journal | author = Xu Z, Mathews DH | title = Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences | journal = Bioinformatics | volume = 27 | issue = 5 | pages = 626–632 | year = 2011 | pmid = 21193521 | doi = 10.1093/bioinformatics/btq726 }}</ref>
|-
! [[Murlet]]
|a multiple alignment tool for RNA sequences using iterative alignment based on Sankoff's algorithm with sharply reduced computational time and memory. || any || yes || yes || no || [http://murlet.ncrna.org/murlet/murlet.html webserver] || <ref name="pmid17459961">{{cite journal | author = Kiryu H, Tabei Y, Kin T, Asai K | title = Murlet: a practical multiple alignment tool for structural RNA sequences | journal = Bioinformatics | volume = 23 | issue = 13 | pages = 1588–98 | year = 2007 | pmid = 17459961 | doi = 10.1093/bioinformatics/btm146 }}</ref>
|-
! [[MXSCARNA]]
|a multiple alignment tool for RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA. || any || yes || yes || no || [http://mxscarna.ncrna.org/mxscarna/mxscarna.html webserver] [http://www.ncrna.org/software/mxscarna/download/ sourcecode] || <ref name="MXSCARNA">{{cite journal | author = Tabei Y, Kiryu H, Kin T, Asai K | title = A fast structural multiple alignment method for long RNA sequences | journal = BMC Bioinformatics | year = 2008 | volume = 33 | url=http://www.biomedcentral.com/1471-2105/9/33}}</ref>
|-
! [[PARTS]]
|A method for joint prediction of alignment and common secondary structures of two RNA sequences using a probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities. || 2 || yes || yes || no || [http://rna.urmc.rochester.edu sourcecode] || <ref name="pmid18304945">{{cite journal |author=Harmanci AO, Sharma G, Mathews DH |title=PARTS: probabilistic alignment for RNA joinT secondary structure prediction. |journal=Nucleic Acids Res |volume=36 |issue=7 |pages=2406–17 |year=2008 |pmid=18304945 |doi=10.1093/nar/gkn043 |pmc=2367733}}</ref>
|-
! [[Pfold]]
|Folds alignments using a SCFG trained on rRNA alignments. ||<math>\le40</math>||input||yes||no||[http://www.daimi.au.dk/~compbio/rnafold/ webserver]||<ref name="pmid10383470">{{cite journal | author = Knudsen B, Hein J | title = RNA secondary structure prediction using stochastic context-free grammars and evolutionary history | journal = Bioinformatics | volume = 15 | issue = 6 | pages = 446–54 | year = 1999 | pmid = 10383470 | doi = 10.1093/bioinformatics/15.6.446 }}</ref><ref name="pmid12824339">{{cite journal | author = Knudsen B, Hein J | title = Pfold: RNA secondary structure prediction using stochastic context-free grammars | journal = Nucleic Acids Res. | volume = 31 | issue = 13 | pages = 3423–8 | year = 2003 | pmid = 12824339 | doi = 10.1093/nar/gkg614 | pmc = 169020 }}</ref>
|-
! [[PETfold]]
|Formally integrates both the energy-based and evolution-based approaches in one model to predict the folding of multiple aligned RNA sequences by a maximum expected accuracy scoring. The structural probabilities are calculated by RNAfold and Pfold. || any || input || yes || no || [http://genome.ku.dk/resources/petfold/ sourcecode] || <ref name="pmid18836192">{{cite journal | author = Seemann S E, Gorodkin J, Backofen R | title = Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments | journal = Nucleic Acids Res. | volume = 36 | issue = 20 | pages = 6355–62 | year = 2008 | pmid = 18836192 | doi = 10.1093/nar/gkn544 | pmc = 2582601 }}</ref>
|-
! [[PMcomp/PMmulti]]
|PMcomp is a variant of Sankoff's algorithm for simultaneous folding and alignment, which takes as input pre-computed base pair probability matrices from McCaskill's algorithm as produced by RNAfold -p. Thus the method can also be viewed as way to compare base pair probability matrices. PMmulti is a wrapper program that does progressive multiple alignments by repeatedly calling pmcomp || <math>2\le seqs \le6</math> || yes || yes || no || [http://www.tbi.univie.ac.at/~ivo/RNA/PMcomp/ sourcecode,] [http://rna.tbi.univie.ac.at/cgi-bin/pmcgi.pl webserver] || <ref name="pmid15073017">{{cite journal | author = Hofacker IL, Bernhart SH, Stadler PF | title = Alignment of RNA base pairing probability matrices | journal = Bioinformatics | volume = 20 | issue = 14 | pages = 2222–7 | year = 2004 | pmid = 15073017 | doi = 10.1093/bioinformatics/bth229 }}</ref>
|-
! [[RNAG]]
|A Gibbs sampling method to determine a conserved structure and the structural alignment. || any || yes || yes || no || [http://ccmbweb.ccv.brown.edu/rnag.html sourcecode] || <ref name="pmid21788211">{{cite journal | author = Wei D, Alpert LV, Lawrence CE | title = RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequence | journal = Bioinformatics | volume = 27 | issue = 18 | pages = 2486–2493 | year = 2011 | pmid = 21788211 | doi = 10.1093/bioinformatics/btr421 }}</ref>
|-
! [[T-Coffee|R-COFFEE]]
|uses RNAlpfold to compute the secondary structure of the provided sequences. A modified version of [[T-Coffee]] is then used to compute the multiple sequence alignment having the best agreement with the sequences and the structures. R-Coffee can be combined with any existing sequence alignment method. || any || yes || yes || no || [http://www.tcoffee.org/Projects_home_page/r_coffee_home_page.html sourcecode,] [http://www.tcoffee.org/ webserver] || <ref name="pmid18420654">{{cite journal |author=Wilm A, Higgins DG, Notredame C |title=R-Coffee: a method for multiple alignment of non-coding RNA |journal=Nucleic Acids Res. |volume=36 |issue=9 |pages=e52 |date=May 2008 |pmid=18420654 |pmc=2396437 |doi=10.1093/nar/gkn174 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=18420654}}</ref><ref name="pmid18483080">{{cite journal |author=Moretti S, Wilm A, Higgins DG, Xenarios I, Notredame C |title=R-Coffee: a web server for accurately aligning noncoding RNA sequences |journal=Nucleic Acids Res. |volume=36 |issue=Web Server issue |pages=W10–3 |date=July 2008 |pmid=18483080 |pmc=2447777 |doi=10.1093/nar/gkn278 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=18483080}}</ref>
|-
! [[TurboFold]]
|This algorithm predicts conserved structures in any number of sequences.  It uses probabilistic alignment and partition functions to map conserved pairs between sequences, and then iterates the partition functions to improve structure prediction accuracy || any || no || yes || yes || [http://rna.urmc.rochester.edu/RNAstructure.html sourcecode] || <ref name="pmid21507242">{{cite journal | author = Harmanci AO, Sharma G, Mathews DH | title = TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequence | journal = BMC Bioinformatics | volume = 12 | pages = 108 | year = 2011 | pmid = 21507242 | doi = 10.1186/1471-2105-12-108 | pmc=3120699}}</ref><ref name="pmid22285566">{{cite journal | author = Seetin MG, Mathews DH | title = TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots | journal = Bioinformatics | volume = 28 | issue = 6 | pages = 792–798 | year = 2012 | pmid = 22285566 | doi = 10.1093/bioinformatics/bts044 }}</ref>
|-
! [[RNA123]]
|The structure based sequence alignment (SBSA) algorithm within RNA123 utilizes a novel suboptimal version of the Needleman-Wunsch global sequence alignment method that fully accounts for secondary structure in the template and query.  It also utilizes two separate substitution matrices that are optimized for RNA helices and single stranded regions.  The SBSA algorithm provides >90% accurate sequence alignments even for structures as large as bacterial 23S rRNA (~2800 nts). || any ||yes || yes || yes || [http://www.rna123.com/ webserver] ||
|-
! [[RNAalifold]]
|Folds precomputed alignments using a combination of free-energy and a covariation measures. Ships with the Vienna package. || any ||input || yes || no || [http://www.tbi.univie.ac.at/~ivo/RNA/ homepage] || <ref name="RNAInverse"/><ref name="pmid12079347">{{cite journal | author = Hofacker IL, Fekete M, Stadler PF | title = Secondary structure prediction for aligned RNA sequences | journal = J. Mol. Biol. | volume = 319 | issue = 5 | pages = 1059–66 | year = 2002 | pmid = 12079347 | doi = 10.1016/S0022-2836(02)00308-X }}</ref>
|-
! [[RNAcast]]
|enumerates the near-optimal abstract shape space, and predicts as the consensus an abstract shape common to all sequences, and for each sequence, the thermodynamically best structure which has this abstract shape. ||any||no||yes||no ||[http://bibiserv.techfak.uni-bielefeld.de/rnacast/ sourcecode,] [http://bibiserv.techfak.uni-bielefeld.de/rnashapes/submission.html webserver]|| <ref name="pmid16020472">{{cite journal | author = Reeder J, Giegerich R | title = Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction | journal = Bioinformatics | volume = 21 | issue = 17 | pages = 3516–23 | year = 2005 | pmid = 16020472 | doi = 10.1093/bioinformatics/bti577 }}</ref>
|-
! [[RNAforester]]
|Compare and align RNA secondary structures via a "forest alignment" approach.||any||yes||input||no||[http://bibiserv.techfak.uni-bielefeld.de/rnaforester/ sourcecode,] [http://bibiserv.techfak.uni-bielefeld.de/rnaforester/submission.html webserver]|| <ref name="pmid16452790">{{cite journal | author = Höchsmann M, Töller T, Giegerich R, Kurtz S | title = Local similarity in RNA secondary structures | journal = Proc IEEE Comput Soc Bioinform Conf | volume = 2 | issue = | pages = 159–68 | year = 2003 | pmid = 16452790 | doi = | issn = }}</ref><ref name="pmid17048408">{{cite journal | author = Höchsmann M, Voss B, Giegerich R | title = Pure multiple RNA secondary structure alignments: a progressive profile approach | journal = IEEE/ACM Trans Comput Biol Bioinform | volume = 1 | issue = 1 | pages = 53–62 | year = 2004 | pmid = 17048408 | doi = 10.1109/TCBB.2004.11 }}</ref>
|-
! [[RNAmine]]
|Frequent stem pattern miner from unaligned RNA sequences is a software tool to extract the structural motifs from a set of RNA sequences. || any || no || yes || no || [http://rnamine.ncrna.org/RNAMINE/ webserver] || <ref name="pmid16908501">{{cite journal | author = Hamada M, Tsuda K, Kudo T, Kin T, Asai K | title = Mining frequent stem patterns from unaligned RNA sequences | journal = Bioinformatics | volume = 22 | issue = 20 | pages = 2480–7 | year = 2006 | pmid = 16908501 | doi = 10.1093/bioinformatics/btl431 }}</ref>
|-
! [[RNASampler]]
|A probabilistic sampling approach that combines intrasequence base pairing probabilities with intersequence base alignment probabilities. This is used to sample possible stems for each sequence and compare these stems between all pairs of sequences to predict a consensus structure for two sequences. The method is extended to predict the common structure conserved among multiple sequences by using a consistency-based score that incorporates information from all the pairwise structural alignments. || any || yes || yes || yes || [http://ural.wustl.edu/~xingxu/RNASampler/index.html sourcecode] || <ref name="pmid17537756">{{cite journal | author = Xu X, Ji Y, Stormo GD | title = RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment | journal = Bioinformatics | volume = 23 | issue = 15 | pages = 1883–91 | year = 2007 | pmid = 17537756 | doi = 10.1093/bioinformatics/btm272 }}</ref>
|-
! [[SCARNA]]
|Stem Candidate Aligner for RNA (Scarna) is a fast, convenient tool for structural alignment of a pair of RNA sequences. It aligns two RNA sequences and calculates the similarities of them, based on the estimated common secondary structures. It works even for pseudoknotted secondary structures.||2||yes||yes||no|| [http://www.scarna.org/scarna/ webserver] || <ref name="pmid16690634">{{cite journal | author = Tabei Y, Tsuda K, Kin T, Asai K | title = SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments | journal = Bioinformatics | volume = 22 | issue = 14 | pages = 1723–9 | year = 2006 | pmid = 16690634 | doi = 10.1093/bioinformatics/btl177 }}</ref>
|-
! [[SimulFold]]
|simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. || any || yes || yes || yes || [http://www.cs.ubc.ca/~irmtraud/simulfold/ sourcecode] || <ref name="pmid17696604">{{cite journal | author = Meyer IM, Miklós I | title = SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework | journal = PLoS Comput. Biol. | volume = 3 | issue = 8 | pages = e149 | year = 2007 | pmid = 17696604 | doi = 10.1371/journal.pcbi.0030149 | pmc = 1941756 |bibcode = 2007PLSCB...3..149M }}</ref>
|-
! [[Stemloc]]
|a program for pairwise RNA structural alignment based on probabilistic models of RNA structure known as Pair [[SCFG|stochastic context-free grammars]].||any||yes||yes||no||[http://biowiki.org/StemLoc sourcecode]||<ref name="pmid15790387">{{cite journal | author = Holmes I | title = Accelerated probabilistic inference of RNA structure evolution | journal = BMC Bioinformatics | volume = 6| pages = 73 | year = 2005 | pmid = 15790387 | doi = 10.1186/1471-2105-6-73 | pmc = 1090553 }}</ref>
|-
! [[StrAl]]
|an alignment tool designed to provide multiple alignments of non-coding RNAs following a fast progressive strategy. It combines the thermodynamic base pairing information derived from RNAfold calculations in the form of base pairing probability vectors with the information of the primary sequence.||<math>\le50</math>||yes||no||no||[http://www.biophys.uni-duesseldorf.de/stral/about.php sourcecode,] [http://www.biophys.uni-duesseldorf.de/stral/advancedForm.php webserver]|| <ref name="pmid16613908">{{cite journal | author = Dalli D, Wilm A, Mainz I, Steger G | title = STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time | journal = Bioinformatics | volume = 22 | issue = 13 | pages = 1593–9 | year = 2006 | pmid = 16613908 | doi = 10.1093/bioinformatics/btl142 }}</ref>
|-
! [[TFold]]
|A tool for predicting non-coding RNA secondary structures including pseudoknots. It takes in input an alignment of RNA sequences and returns the predicted secondary structure(s).It combines criteria of stability, conservation and covariation in order to search for stems and pseudoknots. Users can change different parameters values, set (or not) some known stems (if there are) which are taken into account by the system, choose to get several possible structures or only one, search for pseudoknots or not, etc.
||any||yes||yes||yes||[http://tfold.ibisc.univ-evry.fr:8080/TFold/ webserver]||<ref name="PMID 20047957">{{cite journal | author = Engelen S, Tahi F | title = Tfold: efficient in silico prediction of non-coding RNA secondary structures | journal = Nucleic Acids Res. | volume = 7 | issue = 38| pages = 2453–66 | year = 2010 | pmid = 20047957 | pmc = 2853104 | doi =  10.1093/nar/gkp1067 }}</ref>
|-
! [[WAR (software)|WAR]]
|a webserver that makes it possible to simultaneously use a number of state of the art methods for performing multiple alignment and secondary structure prediction for noncoding RNA sequences. ||<math>2\le seqs \le50</math>||yes||yes||no||[http://genome.ku.dk/resources/war/ webserver]||<ref name="pmid18492721">{{cite journal |author=Torarinsson E, Lindgreen S |title=WAR: Webserver for aligning structural RNAs. |journal=Nucleic Acids Res |volume=36 |issue=Web Server issue |pages=W79–84 |year=2008 |pmid=18492721 |doi=10.1093/nar/gkn275 |pmc=2447782}}</ref>
|-
! [[Xrate]]
|a program for analysis of multiple sequence alignments using phylogenetic [[SCFG|grammars]], that may be viewed as a flexible generalization of the "Pfold" program.||any||yes||yes||no||[http://biowiki.org/XrateSoftware sourcecode]||<ref name="pmid17018148">{{cite journal | author = Klosterman P | title = XRate: a fast prototyping, training and annotation tool for phylo-grammars | journal = BMC Bioinformatics | volume = 7 | pages = 428 | year = 2006 | pmid = 17018148 | doi = 10.1186/1471-2105-7-428 | last2 = Uzilov | first2 = AV | last3 = Bendaña | first3 = YR | last4 = Bradley | first4 = RK | last5 = Chao | first5 = S | last6 = Kosiol | first6 = C | last7 = Goldman | first7 = N | last8 = Holmes | first8 = I | pmc = 1622757 }}</ref>
|-
| colspan=8|
;Notes:{{reflist|group=Note}}
|}
 
==Inter molecular interactions: RNA-RNA==
Many [[ncRNA]]s function by binding to other [[RNA]]s. For example, [[miRNA]]s regulate protein coding gene expression by binding to [[Three prime untranslated region|3' UTRs]], [[snoRNA|small nucleolar RNAs]] guide post-transcriptional modifications by binding to [[rRNA]], [[U4 spliceosomal RNA]] and [[U6 spliceosomal RNA]] bind to each other forming part of the [[spliceosome]] and many small bacterial RNAs regulate gene expression by antisense interactions E.g. [[GcvB RNA|GcvB]], [[OxyS RNA|OxyS]] and [[RyhB RNA|RyhB]].
 
{| class="wikitable sortable"
! Name
! Description || Intra-molecular structure || Comparative || Link || References
|-
! GUUGle
|A utility for fast determination of RNA-RNA matches with perfect hybridization via A-U, C-G, and G-U base pairing.  || no || no || [http://bibiserv.techfak.uni-bielefeld.de/guugle/ webserver] || <ref name="pmid16403789">{{cite journal |doi=10.1093/bioinformatics/btk041 |author=Gerlach W, Giegerich R |title=GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. |journal=Bioinformatics |volume=22 |issue=6 |pages=762–764 |year=2006 |pmid=16403789 }}</ref>
|-
! IntaRNA
|Efficient target prediction incorporating the accessibility of target sites || yes || no || [http://www.bioinf.uni-freiburg.de/Software/#IntaRNA-download sourcecode,] [http://rna.informatik.uni-freiburg.de:8080/v1/IntaRNA.jsp webserver] || <ref name="pmid18940824">{{cite journal |doi=10.1093/bioinformatics/btn544 |author=Busch A, Richter AS, Backofen R |title=IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. |journal=Bioinformatics |volume=24 |issue=24 |pages=2849–56 |year=2008 |pmid=18940824 |pmc=2639303}}</ref><ref name="pmid19850757">{{cite journal |doi=10.1093/bioinformatics/btp609 |author=Richter AS, Schleberger C, Backofen R, Steglich C |title=Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. |journal=Bioinformatics |volume=26 |issue=1 |pages=1–5 |year=2010 |pmid=19850757 |pmc=2796815}}</ref><ref name="pmid20444875">{{cite journal |author=Smith C, Heyne S, Richter AS, Will S, Backofen R |title=Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA. |series=38 |journal=Nucleic Acids Res |volume= Suppl|issue= Web Server|pages= W373–7|year=2010 |pmid=20444875 |pmc=2896085 |doi=10.1093/nar/gkq316}}</ref>
|-
! [[NUPACK]]
| Computes the full unpseudoknotted partition function of interacting strands in dilute solution. Calculates the concentrations, mfes, and base-pairing probabilities of the ordered complexes below a certain complexity. Also computes the partition function and basepairing of single strands including a class of pseudoknotted structures. Also enables design of ordered complexes. || yes || no || [http://nupack.org/ NUPACK] || <ref name="NUPACK">{{cite journal | doi=10.1137/060651100 | author = R.M. Dirks, J.S. Bois, J.M. Schaeffer, E. Winfree, N.A. Pierce | title = Thermodynamic Analysis of Interacting Nucleic Acid Strands | journal =  SIAM Review | volume = 49 | issue=1  | pages = 65–88 | year = 2007|bibcode = 2007SIAMR..49...65D }}</ref>
|-
! [[OligoWalk/RNAstructure]]
|Predicts bimolecular secondary structures with and without intramolecular structure.  Also predicts the hybridization affinity of a short nucleic acid to an RNA target. || yes || no || [http://rna.urmc.rochester.edu] || <ref name="oligowalk">{{cite journal | doi = 10.1017/S1355838299991148 | author = D.H. Mathews, M.E. Burkard, S.M. Freier, D.H. Turner | title = Predicting Oligonucleotide Affinity to RNA Targets. | journal =  RNA | volume = 5  | pages = 1458–1469 | year = 1999 | pmid = 10580474 | issue = 11 | pmc = 1369867}}</ref>
|-
! [[piRNA (software)|piRNA]]
|calculates the partition function and thermodynamics of RNA-RNA interactions. It considers all possible joint secondary structure of two interacting nucleic acids that do not contain pseudoknots, interaction pseudoknots, or zigzags. || yes || no || [http://compbio.cs.sfu.ca/taverna/pirna/ linuxbinary] || <ref name="piRNA">{{cite journal | author = H. Chitsaz, R. Salari, S.C. Sahinalp, R. Backofen | title = A Partition Function Algorithm for Interacting Nucleic Acid Strands. | doi=10.1093/bioinformatics/btp212 | pmc=2687966 | journal =  Bioinformatics | volume = 25 | pages =  | year = 2009 | issue = 12 | pmid=19478011}}</ref>
|-
! [[RNAripalign (software)|RNAripalign]]
|calculates the partition function and thermodynamics of RNA-RNA interactions based on structural alignments. Also supports RNA-RNA interaction prediction for single sequences. It outputs suboptimal structures based on Boltzmann distribution. It considers all possible joint secondary structure of two interacting nucleic acids that do not contain pseudoknots, interaction pseudoknots, or zigzags. || yes || no || [http://www.bioinf.uni-leipzig.de/~qin/resources/ripalign.tar.gz] || <ref name="RNAripalign">{{cite journal | author =Andrew Xiang Li, Jing Qin, Manja Marz, Christian M. Reidys | title = RNA–RNA interaction prediction based on multiple sequence alignments. | doi=10.1093/bioinformatics/btq659 | journal =  Bioinformatics | volume = 27 | pages =  456–463  | year = 2011 | issue = 4 }}</ref>
|-
! [[RactIP]]
|Fast and accurate prediction of RNA-RNA interaction using integer programming. || yes || no || [https://code.google.com/p/ractip/ sourcecode] [http://rna.naist.jp/ractip/ webserver]|| <ref name="pmid20823308">{{cite journal | author = Kato Y, Sato K, Hamada M, Watanabe Y, Asai K, Akutsu T | title = RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming | doi=10.1093/bioinformatics/btq372 | pmc=2935440 | journal =  Bioinformatics | volume = 26 | pages = i460-6 | year = 2010 | issue = 18 | pmid=20823308}}</ref>
|-
! [[RNAaliduplex]]
|Based upon RNAduplex with bonuses for covarying sites || no || yes || [http://www.tbi.univie.ac.at/~ivo/RNA/ sourcecode] || <ref name="RNAInverse"/>
|-
! [[RNAcofold]]
|works much like RNAfold, but allows to specify two RNA sequences which are then allowed to form a dimer structure. || yes || no || [http://www.tbi.univie.ac.at/~ivo/RNA/ sourcecode] || <ref name="RNAInverse"/><ref name="pmid16722605">{{cite journal | author = Bernhart SH, Tafer H, Mückstein U, Flamm C, Stadler PF, Hofacker IL | title = Partition function and base pairing probabilities of RNA heterodimers | journal = Algorithms Mol Biol | volume = 1 | issue = 1 | pages = 3 | year = 2006 | pmid = 16722605 | doi = 10.1186/1748-7188-1-3 | pmc = 1459172 }}</ref>
|-
! [[RNAduplex]]
|computes optimal and suboptimal secondary structures for hybridization. The calculation is simplified by allowing only inter-molecular base pairs. || no || no || [http://www.tbi.univie.ac.at/~ivo/RNA/ sourcecode] || <ref name="RNAInverse"/>
|-
! [[RNAhybrid]]
|a tool for finding the minimum free energy hybridisation of a long and a short RNA. || no || no || [http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/ sourcecode,] [http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html webserver] || <ref name="pmid15383676">{{cite journal | author = Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R | title = Fast and effective prediction of microRNA/target duplexes | journal = RNA | volume = 10 | issue = 10 | pages = 1507–17 | year = 2004 | pmid = 15383676 | doi = 10.1261/rna.5248604 | pmc = 1370637 }}</ref><ref name="pmid16845047">{{cite journal | author = Krüger J, Rehmsmeier M | title = RNAhybrid: microRNA target prediction easy, fast and flexible | journal = Nucleic Acids Res. | volume = 34 | issue = Web Server issue | pages = W451–4 | year = 2006 | pmid = 16845047 | doi = 10.1093/nar/gkl243 | pmc = 1538877 }}</ref>
|-
! [[RNAup]]
|calculates the thermodynamics of RNA-RNA interactions. RNA-RNA binding is decomposed into two stages. (1) First the probability that a sequence interval (e.g. a binding site) remains unpaired is computed. (2) Then the binding energy given that the binding site is unpaired is calculated as the optimum over all possible types of bindings. || yes || no || [http://www.tbi.univie.ac.at/~ivo/RNA/ sourcecode] || <ref name="RNAInverse"/><ref name="pmid16446276">{{cite journal | author = Mückstein U, Tafer H, Hackermüller J, Bernhart SH, Stadler PF, Hofacker IL | title = Thermodynamics of RNA-RNA binding | journal = Bioinformatics | volume = 22 | issue = 10 | pages = 1177–82 | year = 2006 | pmid = 16446276 | doi = 10.1093/bioinformatics/btl024 }}</ref>
|}
 
==Inter molecular interactions: MicroRNA:UTR==
[[miRNA|MicroRNAs]] regulate protein coding gene expression by binding to [[Three prime untranslated region|3' UTRs]], there are tools specifically designed for predicting these interactions. For an evaluation of target prediction methods on high-throughput experimental data see (Baek ''et al.'', Nature 2008) <ref name="pmid18668037">{{cite journal |author=Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP |title=The impact of microRNAs on protein output. |journal=Nature |volume=455 |issue=7209 |pages=64–71 |year=2008 |pmid=18668037 |doi=10.1038/nature07242 }}</ref> and (Alexiou ''et al.'', Bioinformatics 2009)<ref name="pmid19789267">{{cite journal |author=Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG |title=Lost in translation: an assessment and perspective for computational microRNA target identification. |journal=Bioinformatics |volume=25 |issue=23 |pages=3049–55 |year=2009 |pmid=19789267 |doi=10.1093/bioinformatics/btp565}}</ref>
 
{| class="wikitable sortable"
! Name
! Description ||Species Specific || Intra-molecular structure || Comparative || Link || References
|-
! [[Diana-microT]]
|DIANA-microT 3.0 is an algorithm based on several parameters calculated individually for each microRNA and it combines conserved and non-conserved microRNA recognition elements into a final prediction score.|| human, mouse || no || yes || [http://diana.cslab.ece.ntua.gr/microT/ webserver] || <ref name="pmid19765283">{{cite journal |author= Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG |title=Accurate microRNA target prediction correlates with protein repression levels. |journal=BMC Bioinformatics |volume=10|pages=295 |year=2009 |pmid=19765283 |doi=10.1186/1471-2105-10-295|pmc=2752464}}</ref>
|-
! [[MicroTar]]
|An animal miRNA target prediction tool based on miRNA-target complementarity and thermodynamic data. || no || no || no || [http://tiger.dbs.nus.edu.sg/microtar/ sourcecode] || <ref name="pmid17254305">{{cite journal |author=Thadani R, Tammi MT |title=MicroTar: predicting microRNA targets from RNA duplexes. |series=7 |journal=BMC Bioinformatics |volume=Suppl 5|pages=S20 |year=2006 |pmid=17254305 |doi=10.1186/1471-2105-7-S5-S20 |pmc=1764477}}</ref>
|-
! [[miTarget]]
|microRNA target gene prediction using a support vector machine. || no || no || no || [http://cbit.snu.ac.kr/~miTarget/ webserver] || <ref name="pmid16978421">{{cite journal |author=Kim SK, Nam JW, Rhee JK, Lee WJ, Zhang BT |title=miTarget: microRNA target gene prediction using a support vector machine. |journal=BMC Bioinformatics |volume=7|pages=411 |year=2006 |pmid=16978421 |doi=10.1186/1471-2105-7-411 |pmc=1594580}}</ref>
|-
! [[miRror]]
| Based on the notion of a combinatorial regulation by an ensemble of miRNAs or genes. miRror integrates predictions from a dozen of miRNA resources that are based on complementary algorithms into a unified statistical framework || no || no || no || [http://www.proto.cs.huji.ac.il/mirror/index.php  webserver] || <ref>{{cite doi|10.1093/bioinformatics/btq298}}</ref><ref>{{cite doi|10.1093/nar/gks759}}</ref>
|-
! [[PicTar]]
|Combinatorial microRNA target predictions. || 8 vertebrates || no || yes || [http://pictar.bio.nyu.edu predictions] || <ref name="pmid15806104">{{cite journal |author=Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N |title=Combinatorial microRNA target predictions. |journal=Nat Genet |volume=37 |issue=5 |pages=495–500 |year=2005 |pmid=15806104 |doi=10.1038/ng1536}}</ref>
|-
! [[PITA (software)|PITA]]
|Incorporates the role of target-site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition.|| no || yes || no || [http://genie.weizmann.ac.il/pubs/mir07/mir07_exe.html executable,] [http://genie.weizmann.ac.il/pubs/mir07/mir07_prediction.html webserver,] [http://genie.weizmann.ac.il/pubs/mir07/mir07_data.html predictions] || <ref name="pmid17893677">{{cite journal |author=Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E |title=The role of site accessibility in microRNA target recognition. |journal=Nat Genet |volume=39 |issue=10 |pages=1278–84 |year=2007 |pmid=17893677 |doi=10.1038/ng2135}}</ref>
|-
! [[RNA22]]
|The first link (predictions) provides RNA22 predictions for all protein coding transcripts in human, mouse, roundworm, and fruit fly. It allows you to visualize the predictions within a cDNA map and also find transcripts where multiple miR's of interest target. The second web-site link (custom) first finds putative microRNA binding sites in the sequence of interest, then identifies the targeted microRNA. || no || no || no || [http://cm.jefferson.edu/rna22v1.0/ predictions] [http://cbcsrv.watson.ibm.com/rna22.html custom] || <ref name="pmid16990141">{{cite journal |author=Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I |title=A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. |journal=Cell |volume=126 |issue=6 |pages=1203–17 |year=2006 |pmid=16990141 |doi=10.1016/j.cell.2006.07.031}}</ref>
|-
! [[RNAhybrid]]
|a tool for finding the minimum free energy hybridisation of a long and a short RNA. || no || no || no || [http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/ sourcecode,] [http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html webserver] || <ref name="pmid15383676"/><ref name="pmid16845047"/>
|-
! [[Sylamer]]
|Sylamer is a method for finding significantly over or under-represented words in sequences according to a sorted gene list. Typically it is used to find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data. || no || no || no || [http://www.ebi.ac.uk/enright/sylamer/ sourcecode] [http://www.ebi.ac.uk/enright/sylarray/ webserver] || <ref name="pmid18978784">{{cite journal |author=van Dongen S, Abreu-Goodger C, Enright AJ |title=Detecting microRNA binding and siRNA off-target effects from expression data. |journal=Nat Methods |volume=5 |issue=12 |pages=1023–5 |year=2008 |pmid=18978784 |doi=10.1038/nmeth.1267 |pmc=2635553}}</ref><ref name="pmid20871108">{{cite journal |author=Bartonicek N, Enright AJ |title=SylArray: A web-server for automated detection of miRNA effects from expression data. |journal=Bioinformatics |year=2010 |pmid=20871108 |doi=10.1093/bioinformatics/btq545 |volume=26 |issue=22 |pages=2900–1}}</ref>
|-
! [[TAREF]]
|TAREF stands for TARget REFiner. It predicts microRNA targets on the basis of multiple feature information derived from the flanking regions of the predicted target sites where traditional structure prediction approach may not be successful to assess the openness. It also provides an option to use encoded pattern to refine filtering. || Yes || no || no || [http://scbb.ihbt.res.in/TAREF/programchoice.html server/sourcecode] || <ref name="pmid=20413915">{{cite journal |doi=10.1007/s12038-010-0013-7 |author=R. Heikham and R. Shankar |title=Flanking region sequence information to refine microRNA target predictions. |journal=Journal of Biosciences |volume=35 |issue=1 |pages=105–18|year=2010 |pmid=20413915}}</ref>
|-
! [[p-TAREF]]
|p-TAREF stands for plant TARget REFiner. It identifies plant microRNA targets on the basis of multiple feature information derived from the flanking regions of the predicted target sites where traditional structure prediction approach may not be successful to assess the openness. It also provides an option to use encoded pattern to refine filtering.  It first time employed power of machine learning approach with scoring scheme through Support Vector Regression(SVR) while considering structural and alignment aspects of targeting in plants with plant specific models. p-TAREF has been implemented in concurrent architecture in server as well as standalone form, making it one of the very few available target identification tools able to run concurrently on simple desktops while performing huge transcriptome level analysis accurately and fast. Besides this, it also provides an option to experimentally validate the predicted targets, on the spot, using expression data, which has been integrated in its back-end, to draw confidence on prediction along with SVR score.p-TAREF performance benchmarking has been done extensively through different tests and compared with other plant miRNA target identification tools. p-TAREF was found better performing.|| Yes || no || no || [http://scbb.ihbt.res.in/SCBB_dept/Software.php server/standalone] ||
|-
! [[TargetScan]]
|Predicts biological targets of miRNAs by searching for the presence of sites that match the seed region of each miRNA. In flies and nematodes, predictions are ranked based on the probability of their evolutionary conservation.  In zebrafish, predictions are ranked based on site number, site type, and site context, which includes factors that influence target-site accessibility.  In mammals, the user can choose whether the predictions should be ranked based on the probability of their conservation or on site number, type, and context.  In mammals and nematodes, the user can chose to extend the predictions beyond conserved sites and consider all sites. || vertebrates, flies, nematodes || evaluated indirectly || yes || [http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_60 sourcecode], [http://www.targetscan.org/ webserver] || <ref name="pmid14697198">{{cite journal |author=Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB |title=Prediction of mammalian microRNA targets. |journal=Cell |volume=115 |issue=7 |pages=787–98 |year=2003 |pmid=14697198 |doi=10.1016/S0092-8674(03)01018-3}}</ref><ref name="pmid15652477">{{cite journal |author=Lewis BP, Burge CB, Bartel DP |title=Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. |journal=Cell |volume=120 |issue=1 |pages=15–20 |year=2005 |pmid=15652477 |doi=10.1016/j.cell.2004.12.035}}</ref><ref name="pmid17612493">{{cite journal |author=Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP |title=MicroRNA targeting specificity in mammals: determinants beyond seed pairing. |journal=Mol Cell |volume=27 |issue=1 |pages=91–105 |year=2007 |pmid=17612493 |doi=10.1016/j.molcel.2007.06.017}}</ref><ref name="pmid21909094">{{cite journal |author=Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP |title=Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. |journal=Nature Structural & Molecular Biology |volume=18 |issue=10 |pages=1139–1146 |year=2011 |pmid=21909094 |doi=10.1038/nsmb.2115 |pmc=3190056}}</ref>
|}
 
==ncRNA gene prediction software==
{| class="wikitable sortable"
! Name
! Description
! Number of sequences<br/><ref group=Note>'''Number of sequences:''' <any|num>.</ref>
! Alignment<br/><ref group=Note>'''Alignment:''' predicts an [[sequence alignment|alignment]], <input|yes|no>.</ref>
! Structure<br/><ref group=Note>'''Structure:''' predicts [[RNA structure|structure]], <input|yes|no>.</ref>
! Link || References
|-
! [[Alifoldz]]
|Assessing a multiple sequence alignment for the existence of an unusual stable and conserved RNA secondary structure. || any || input || yes || [http://www.tbi.univie.ac.at/papers/SUPPLEMENTS/Alifoldz/ sourcecode] || <ref name="pmid15313604">{{cite journal | author = Washietl S, Hofacker IL | title = Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics | journal = J. Mol. Biol. | volume = 342 | issue = 1 | pages = 19–30 | year = 2004 | pmid = 15313604 | doi = 10.1016/j.jmb.2004.07.018 }}</ref>
|-
! [[EvoFold]]
|a comparative method for identifying functional RNA structures in multiple-sequence alignments. It is based on a probabilistic model-construction called a phylo-SCFG and exploits the characteristic differences of the substitution process in stem-pairing and unpaired regions to make its predictions. || any || input || yes || [http://www.cbse.ucsc.edu/~jsp/EvoFold/ linuxbinary] || <ref name="pmid16628248">{{cite journal | author = Pedersen JS, Bejerano G, Siepel A, ''et al.'' | title = Identification and classification of conserved RNA secondary structures in the human genome | journal = PLoS Comput. Biol. | volume = 2 | issue = 4 | pages = e33 | year = 2006 | pmid = 16628248 | doi = 10.1371/journal.pcbi.0020033 | pmc = 1440920 |bibcode = 2006PLSCB...2...33P }}</ref>
|-
! [[GraphClust]]
|Fast RNA structural clustering method to identify common (local) RNA secondary structures. Predicted structural clusters are presented as alignment. Due to the linear time complexity for clustering it is possible to analyse large RNA datasets. || any || yes || yes || [http://www.bioinf.uni-freiburg.de/Software/GraphClust/ sourcecode]|| <ref name="pmid22689765">{{cite journal | author = Heyne S, Costa F, Rose D, Backofen R | title = GraphClust: alignment-free structural clustering of local RNA secondary structures | journal = Bioinformatics | volume = 28 | issue = 12 | pages = i224-i232 | year = 2012 | pmid = 22689765 | doi = 10.1093/bioinformatics/bts224 }}</ref>
|-
! [[MSARi]]
|heuristic search for statistically significant conservation of RNA secondary structure in deep multiple sequence alignments. || any || input || yes || [http://theory.csail.mit.edu/MSARi sourcecode] || <ref>{{cite journal | author = Coventry A, Kleitman DJ, Berger BA | title = MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure | journal = PNAS | volume = 101 | issue = 33 | pages = 12102–12107 | pmid = 15304649 | doi = 10.1073/pnas.0404193101| year = 2004 | pmc = 514400 |bibcode = 2004PNAS..10112102C }}</ref>
|-
! [[QRNA]]
|This is the code from Elena Rivas that accompanies a submitted manuscript "Noncoding RNA gene detection using camparative sequence analysis". QRNA uses comparative genome sequence analysis to detect conserved RNA secondary structures, including both ncRNA genes and cis-regulatory RNA structures. || 2 || input || yes || [http://selab.janelia.org/software.html sourcecode] || <ref name="pmid11801179">{{cite journal | author = Rivas E, Eddy SR | title = Noncoding RNA gene detection using comparative sequence analysis | journal = BMC Bioinformatics | volume = 2| pages = 8 | year = 2001 | pmid = 11801179 | doi = 10.1186/1471-2105-2-8 | pmc = 64605 }}</ref><ref name="pmid11553332">{{cite journal | author = Rivas E, Klein RJ, Jones TA, Eddy SR | title = Computational identification of noncoding RNAs in E. coli by comparative genomics | journal = Curr. Biol. | volume = 11 | issue = 17 | pages = 1369–73 | year = 2001 | pmid = 11553332 | doi = 10.1016/S0960-9822(01)00401-8 }}</ref>
|-
! [[RNAz]]
|program for predicting structurally conserved and thermodynamic stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs. || any || input || yes || [http://www.tbi.univie.ac.at/~wash/RNAz/ sourcecode,] [http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi webserver] [http://psb.stanford.edu/psb-online/proceedings/psb10/abstracts/2010_p69.html RNAz 2] || <ref name="pmid15665081">{{cite journal | author = Washietl S, Hofacker IL, Stadler PF | title = Fast and reliable prediction of noncoding RNAs | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 102 | issue = 7 | pages = 2454–9 | year = 2005 | pmid = 15665081 | doi = 10.1073/pnas.0409169102 | pmc = 548974 |bibcode = 2005PNAS..102.2454W }}</ref><ref name="pmid17452347">{{cite journal | author = Gruber AR, Neuböck R, Hofacker IL, Washietl S | title = The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures | journal = Nucleic Acids Res. | volume = 35 | issue = Web Server issue | pages = W335–8 | year = 2007 | pmid = 17452347 | doi = 10.1093/nar/gkm222 | pmc = 1933143 }}</ref><ref name="pmid17993695">{{cite journal | author = Washietl S | title = Prediction of Structural Noncoding RNAs With RNAz | journal = Methods Mol. Biol. | volume = 395 | issue = | pages = 503–26 | year = 2007 | pmid = 17993695 | doi = 10.1007/978-1-59745-514-5_32| issn = }}</ref>
|-
! [[Xrate]]
|a program for analysis of multiple sequence alignments using phylogenetic [[SCFG|grammars]], that may be viewed as a flexible generalization of the "Evofold" program.||any||yes||yes||[http://biowiki.org/XrateSoftware sourcecode]||<ref name="pmid17018148"/>
|-
| colspan=7|
;Notes:{{reflist|group=Note}}
|}
 
==Family specific gene prediction software==
{| class="wikitable sortable"
! Name
! Description || Family || Link || References
|-
! ARAGORN
|ARAGORN detects tRNA and tmRNA in nucleotide sequences. || [[tRNA]] [[tmRNA]] || [http://130.235.46.10/ARAGORN/ webserver] [http://130.235.46.10/ARAGORN/aragorn1.2.28.c source] || <ref name="pmid14704338">{{cite journal |author=Laslett D, Canback B |title=ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. |journal=Nucl. Acids Res. |volume=32 |issue= 1|pages=39 |year=2004 |pmid=14704338 |doi=10.1093/nar/gkh152|pmc=373265}}</ref>
|-
! miReader
|miReader is a first of its type to detect mature miRNAs without any dependence upon genomic or reference sequences. So far, discovering miRNAs was possible only with species for which genomic or reference sequences would be available as most of the miRNA discovery tools relied on drawing pre-miRNA candidates. Due to this, miRNA biology became limited to model organisms, mostly. With miReader, one can now directly find out mature miRNAs from small RNA sequencing data, without any need of genomic/reference sequences. It has been developed for large number of Phyla and species, ranging from Vertebrate models to plant and fish models. Its accuracy has been found to be consistently >90% for large number of validatory testing. || [[mature miRNA]] || [http://scbb.ihbt.res.in/2810-12/miReader.php webserver/source] [http://sourceforge.net/projects/mireader/ webserver/source] || <ref name="pmid23805282">{{cite journal |author=Jha A, Shankar R |title=miReader: Discovering novel miRNAs in species without sequenced genome. |journal=PLOS ONE. |volume=8 |issue= 6|pages= e66857|year=2013 |pmid=23805282 |doi= 10.1371/journal.pone.0066857|pmc=3689854
}}</ref>
|-
 
! [[miRNAminer]]
|Given a search query, candidate homologs are identified using BLAST search and then tested for their known miRNA properties, such as secondary structure, energy, alignment and conservation, in order to assess their fidelity. || [[MicroRNA]] || [http://groups.csail.mit.edu/pag/mirnaminer/ webserver] || <ref name="pmid18215311">{{cite journal |author=Artzi S, Kiezun A, Shomron N |title=miRNAminer: a tool for homologous microRNA gene search. |journal=BMC Bioinformatics |volume=9|pages=39 |year=2008 |pmid=18215311 |doi=10.1186/1471-2105-9-39 |pmc=2258288}}</ref>
|-
! RISCbinder
|Prediction of guide strand of microRNAs. || [[MicroRNA|Mature miRNA]] || [http://crdd.osdd.net:8081/RISCbinder/ webserver] || <ref name=riscbinder>{{cite journal |author=Ahmed F, Ansari HR and Raghava GPS |title=Prediction of guide strand of microRNAs from its sequence and secondary structure |journal=BMC Bioinformatics |year=2009 |url=http://www.biomedcentral.com/1471-2105/10/105}}</ref>
|-
! [[RNAmicro]]
|A SVM-based approach that, in conjunction with a non-stringent filter for consensus secondary structures, is capable of recognizing microRNA precursors in multiple sequence alignments. || [[MicroRNA]] || [http://www.bioinf.uni-leipzig.de/~jana/software/RNAmicro.html homepage] || <ref name="pmid16873472">{{cite journal |author=Hertel J, Stadler PF |title=Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. |journal=Bioinformatics |volume=22 |issue=14 |pages=e197–202 |year=2006 |pmid=16873472 |doi=10.1093/bioinformatics/btl257}}</ref>
|-
! RNAmmer
|RNAmmer uses [[HMMER]] to annotate [[rRNA]] genes in genome sequences. Profiles were built using alignments from the European ribosomal RNA database<ref name="pmid14681368">{{cite journal |author=Wuyts J, Perrière G, Van De Peer Y |title=The European ribosomal RNA database. |journal=Nucleic Acids Res |volume=32 |issue=Database issue |pages=D101–3 |year=2004 |pmid=14681368 |doi=10.1093/nar/gkh065 |pmc=308799}}</ref> and the 5S Ribosomal RNA Database.<ref name="pmid11752286">{{cite journal |doi=10.1093/nar/30.1.176 |author=Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J |title=5S Ribosomal RNA Database. |journal=Nucleic Acids Res |volume=30 |issue=1 |pages=176–8 |year=2002 |pmid=11752286 |pmc=99124}}</ref>|| [[rRNA]] || [http://www.cbs.dtu.dk/services/RNAmmer/ webserver] [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?rnammer source] || <ref name="pmid17452365">{{cite journal |author=Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW |title=RNAmmer: consistent and rapid annotation of ribosomal RNA genes. |journal=Nucleic Acids Res |volume=35 |issue=9 |pages=3100–8 |year=2007 |pmid=17452365 |doi=10.1093/nar/gkm160 |pmc=1888812}}</ref>
|-
! [[SnoReport]]
|Uses a combination of RNA secondary structure prediction and machine learning that is designed to recognize the two major classes of snoRNAs, box C/D and box H/ACA snoRNAs, among ncRNA candidate sequences. || [[snoRNA]] || [http://www.bioinf.uni-leipzig.de/~jana/software/SnoReport.html sourcecode] || <ref name="pmid17895272">{{cite journal |author=Hertel J, Hofacker IL, Stadler PF |title=SnoReport: computational identification of snoRNAs with unknown targets. |journal=Bioinformatics |volume=24 |issue=2 |pages=158–64 |year=2008 |pmid=17895272 |doi=10.1093/bioinformatics/btm464}}</ref>
|-
! [[SnoScan]]
|Search for C/D box methylation guide snoRNA genes in a genomic sequence. || [[snoRNA|C/D box snoRNA]] || [http://lowelab.ucsc.edu/snoscan/ sourcecode,] [http://lowelab.ucsc.edu/snoscan/ webserver] || <ref name="pmid10024243">{{cite doi|10.1126/science.283.5405.1168}}</ref><ref name="pmid15980563">{{cite journal |author=Schattner P, Brooks AN, Lowe TM |title=The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. |journal=Nucleic Acids Res |volume=33 |issue=Web Server issue |pages=W686–9 |year=2005 |pmid=15980563 |doi=10.1093/nar/gki366 |pmc=1160127}}</ref>
|-
! [[snoSeeker]]
|snoSeeker includes two snoRNA-searching programs, CDseeker and ACAseeker, specific to the detection of C/D [[snoRNA]]s and H/ACA snoRNAs, respectively. snoSeeker has been used to scan four human–mammal whole-genome alignment (WGA) sequences and identified 54 novel candidates including 26 orphan candidates as well as 266 known snoRNA genes. || [[snoRNA]] || [http://genelab.sysu.edu.cn/snoSeeker/index.php webserver,stand-alone] || <ref name="pmid16990247">{{cite journal |author=Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH. |title=snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. |journal=Nucleic Acids Res. |volume=34 |issue=18 |pages=5112–5123 |year=2006 |pmid=16990247 |pmc=1636440 |doi=10.1093/nar/gkl672}}</ref>
|-
! [[tRNAscan-SE]]
|a program for the detection of transfer RNA genes in genomic sequence. || [[tRNA]] || [http://lowelab.ucsc.edu/tRNAscan-SE/ sourcecode,] [http://lowelab.ucsc.edu/tRNAscan-SE/ webserver] || <ref name="pmid15980563"/><ref name="pmid9023104">{{cite journal |author=Lowe TM, Eddy SR |title=tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. |journal=Nucleic Acids Res |volume=25 |issue=5 |pages=955–64 |year=1997 |pmid=9023104 |doi=10.1093/nar/25.5.955 |pmc=146525}}</ref>
|-
! [[miRNAFold]]
|A fast ab initio software for searching for microRNA precursors in genomes. || [[microRNA]] || [http://EvryRNA.ibisc.univ-evry.fr/ webserver] || <ref name="pmid22362754">{{cite journal |author=Tempel S, Tahi F |title=A fast ab-initio method for predicting miRNA precursors in genomes. |journal=Nucleic Acids Res. |volume=40 |issue=11 |pages=955–64 |year=2012 |pmid=22362754 |doi= 10.1093/nar/gks146 |pmc=3367186}}</ref>
|-
|}
 
==RNA homology search software==
{| class="wikitable sortable"
! Name
! Description || Link || References
|-
! [[ERPIN]]
|"Easy RNA Profile IdentificatioN" is an RNA motif search program reads a sequence alignement and secondary structure, and automatically infers a statistical "secondary structure profile" (SSP). An original Dynamic Programming algorithm then matches this SSP onto any target database, finding solutions and their associated scores. || [http://rna.igmors.u-psud.fr/erpin/ sourcecode] [http://tagc.univ-mrs.fr/erpin/ webserver] || <ref name="pmid11700055">{{cite journal |author=Gautheret D, Lambert A |title=Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. |journal=J Mol Biol |volume=313 |issue=5 |pages=1003–11 |year=2001 |pmid=11700055 |doi=10.1006/jmbi.2001.5102}}</ref><ref name="pmid15215371">{{cite journal |author=Lambert A, Fontaine JF, Legendre M, Leclerc F, Permal E, Major F, Putzer H, Delfour O, Michot B, Gautheret D |title=The ERPIN server: an interface to profile-based RNA motif identification. |journal=Nucleic Acids Res |volume=32 |issue=Web Server issue |pages=W160–5 |year=2004 |pmid=15215371 |doi=10.1093/nar/gkh418 |pmc=441556}}</ref><ref name="pmid15892887">{{cite journal |author=Lambert A, Legendre M, Fontaine JF, Gautheret D |title=Computing expectation values for RNA motifs using discrete convolutions. |journal=BMC Bioinformatics |volume=6|pages=118 |year=2005 |pmid=15892887 |doi=10.1186/1471-2105-6-118 |pmc=1168889}}</ref>
|-
! [[Infernal (software)|Infernal]]
|"INFERence of RNA ALignment" is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). || [http://infernal.janelia.org/ sourcecode] || <ref name="pmid17397253">{{cite journal |author=Nawrocki EP, Eddy SR |title=Query-dependent banding (QDB) for faster RNA similarity searches. |journal=PLoS Comput Biol |volume=3 |issue=3 |pages=e56 |year=2007 |pmid=17397253 |doi=10.1371/journal.pcbi.0030056 |pmc=1847999|bibcode = 2007PLSCB...3...56N }}</ref><ref name="pmid12095421">{{cite journal |author=Eddy SR |title=A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. |journal=BMC Bioinformatics |volume=3|pages=18 |year=2002 |pmid=12095421 |doi=10.1186/1471-2105-3-18 |pmc=119854}}</ref><ref name="pmid8029015">{{cite journal |author=Eddy SR, Durbin R |title=RNA sequence analysis using covariance models. |journal=Nucleic Acids Res |volume=22 |issue=11 |pages=2079–88 |year=1994 |pmid=8029015 |doi=10.1093/nar/22.11.2079 |pmc=308124}}</ref>
|-
! [[GraphClust]]
|Fast RNA structural clustering method to identify common (local) RNA secondary structures. Predicted structural clusters are presented as alignment. Due to the linear time complexity for clustering it is possible to analyse large RNA datasets. || [http://www.bioinf.uni-freiburg.de/Software/GraphClust/ sourcecode]|| <ref name="pmid22689765">{{cite journal | author = Heyne S, Costa F, Rose D, Backofen R | title = GraphClust: alignment-free structural clustering of local RNA secondary structures | journal = Bioinformatics | volume = 28 | issue = 12 | pages = i224-i232 | year = 2012 | pmid = 22689765 | doi = 10.1093/bioinformatics/bts224 }}</ref>
|-
! [[PHMMTS]]
|"pair hidden Markov models on tree structures" is an extension of pair hidden Markov models defined on alignments of trees. || [http://phmmts.dna.bio.keio.ac.jp/ sourcecode,] [http://phmmts.dna.bio.keio.ac.jp/ webserver] || <ref name="pmid16204111">{{cite journal |author=Sato K, Sakakibara Y |title=RNA secondary structural alignment with conditional random fields. |series=21 |journal=Bioinformatics |volume=Suppl 2 |issue= suppl_2|pages=ii237–42 |year=2005 |pmid=16204111 |doi=10.1093/bioinformatics/bti1139}}</ref>
|-
! [[RaveNnA]]
|A slow and rigorous or fast and heuristic sequence-based filter for covariance models. || [http://bliss.biology.yale.edu/~zasha/ravenna/ sourcecode] || <ref name="pmid15262817">{{cite journal |author=Weinberg Z, Ruzzo WL |title=Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. |series=20 |journal=Bioinformatics |volume=Suppl 1 |issue= suppl_1|pages=i334–41 |year=2004 |pmid=15262817 |doi=10.1093/bioinformatics/bth925}}</ref><ref name="pmid16267089">{{cite journal |author=Weinberg Z, Ruzzo WL |title=Sequence-based heuristics for faster annotation of non-coding RNA families. |journal=Bioinformatics |volume=22 |issue=1 |pages=35–9 |year=2006 |pmid=16267089 |doi=10.1093/bioinformatics/bti743}}</ref>
|-
! [[RSEARCH]]
|Takes a single RNA sequence with its secondary structure and utilizes a local alignment algorithm to search a database for homologous RNAs. || [ftp://selab.janelia.org/pub/software/rsearch/ sourcecode] || <ref name="pmid14499004">{{cite journal |author=Klein RJ, Eddy SR |title=RSEARCH: finding homologs of single structured RNA sequences. |journal=BMC Bioinformatics |volume=4|pages=44 |year=2003 |pmid=14499004 |doi=10.1186/1471-2105-4-44 |pmc=239859}}</ref>
|-
! [[Structator]]
|Ultra fast software for searching for RNA structural motifs employing an innovative index-based bidirectional matching algorithm combined with a new fast fragment chaining strategy. || [http://www.zbh.uni-hamburg.de/Structator/ sourcecode] || <ref name="pmid21619640">{{cite journal |author=Meyer F, Kurtz S, Backofen R, Will S, Beckstette M |title=Structator: fast index-based search for RNA sequence-structure patterns |journal=BMC Bioinformatics |volume=12|pages=214 |year=2011 |pmid=21619640 |doi=10.1186/1471-2105-12-214 |pmc=3154205}}</ref>
|}
 
==Benchmarks==
{| class="wikitable sortable"
! Name
! Description
! Structure<ref group=Note>'''Structure:''' benchmarks [[RNA structure|structure]] prediction tools <yes|no>.</ref>
! Alignment<ref group=Note>'''Alignment:'''  benchmarks [[sequence alignment|alignment]] tools <yes|no>.</ref>
! Phylogeny || Links || References
|-
! [[BRalibase]] I
|A comprehensive comparison of comparative RNA structure prediction approaches || yes || no || no || [http://projects.binf.ku.dk/pgardner/bralibase/bralibase1.html data] || <ref name="pmid15458580">{{cite journal | author = Gardner PP, Giegerich R | title = A comprehensive comparison of comparative RNA structure prediction approaches | journal = BMC Bioinformatics | volume = 5| pages = 140 | year = 2004 | pmid = 15458580 | doi = 10.1186/1471-2105-5-140 | pmc = 526219 }}</ref>
|-
! BRalibase II
|A benchmark of multiple sequence alignment programs upon structural RNAs || no || yes || no || [http://projects.binf.ku.dk/pgardner/bralibase/bralibase2.html data] || <ref name="pmid15860779">{{cite journal | author = Gardner PP, Wilm A, Washietl S | title = A benchmark of multiple sequence alignment programs upon structural RNAs | journal = Nucleic Acids Res. | volume = 33 | issue = 8 | pages = 2433–9 | year = 2005 | pmid = 15860779 | doi = 10.1093/nar/gki541 | pmc = 1087786 }}</ref>
|-
! BRalibase 2.1
|A benchmark of multiple sequence alignment programs upon structural RNAs || no || yes || no || [http://www.biophys.uni-duesseldorf.de/bralibase/ data] || <ref name="pmid17062125">{{cite journal |author=Wilm A, Mainz I, Steger G |title=An enhanced RNA alignment benchmark for sequence alignment programs. |journal=Algorithms Mol Biol |volume=1 |issue= 1|pages=19 |year=2006 |pmid=17062125 |pmc=1635699 |doi=10.1186/1748-7188-1-19}}</ref>
|-
! BRalibase III
|A critical assessment of the performance of homology search methods on noncoding RNA || no || yes || no || [http://projects.binf.ku.dk/pgardner/bralibase/bralibase3 data] || <ref name="pmid17151342">{{cite journal | author = Freyhult EK, Bollback JP, Gardner PP | title = Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA | journal = Genome Res. | volume = 17 | issue = 1 | pages = 117–25 | year = 2007 | pmid = 17151342 | doi = 10.1101/gr.5890907 | pmc = 1716261 }}</ref>
|-
! CompaRNA
|An independent comparison of single-sequence and comparative methods for RNA secondary structure prediction || yes || no || no || [http://comparna.amu.edu.pl AMU mirror] or [http://iimcb.genesilico.pl/comparna/ IIMCB mirror] || <ref name="pmid23435231">{{cite journal | author = Puton T, Kozlowski LP, Rother KM, Bujnicki JM | title = CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction | journal = Nucleic Acids Research | volume = 41 | issue = 7 | pages = 4307–23 | year =  2013 | pmid = 23435231 | doi = 10.1093/nar/gkt101 }}</ref>
|-
| colspan=7|
;Notes:{{reflist|group=Note}}
|}
 
==Alignment viewers/editors==
{| class="wikitable sortable"
! Name
! Description
! Alignment<ref group=Note>'''Alignment:''' view and edit an [[sequence alignment|alignment]], <yes|no>.</ref>
! Structure<ref group=Note>'''Structure:''' view and edit [[RNA structure|structure]], <yes|no>.</ref>
! Link || References
|-
! [[4sale]]
|A tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing||yes||yes || [http://4sale.bioapps.biozentrum.uni-wuerzburg.de/index.html sourcecode] || <ref name="pmid17101042">{{cite journal | author = Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M | title = 4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing | journal = BMC Bioinformatics | volume = 7| pages = 498 | year = 2006 | pmid = 17101042 | doi = 10.1186/1471-2105-7-498 | pmc = 1637121 }}</ref>
|-
! [[Colorstock]], [[SScolor]], [[Raton (software)|Raton]]
|Colorstock, a command-line script using ANSI terminal color; SScolor, a Perl script that generates static HTML pages; and Raton, an AJAX web application generating dynamic HTML. Each tool can be used to color RNA alignments by secondary structure and to visually highlight compensatory mutations in stems. || yes || yes || [http://biowiki.org/RNAAlignmentViewers sourcecode] || <ref name="colorstock">{{cite journal | author =  Bendana YR, Holmes IH | title = Colorstock, SScolor, Rat  ́on: RNA Alignment Visualization Tools |doi=10.1093/bioinformatics/btm635| pmid=18218657 |journal = Bioinformatics | year = 2008 | volume=24 | issue=4 | pages=579–80}}</ref>
|-
! [[Integrated Genome Browser]] (IGB)
|a multiple alignment viewer written in Java.
||yes||no|| [http://genoviz.sourceforge.net/ sourcecode] || <ref name='binf_igb_paper'>{{cite journal |author=Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE |title=The Integrated Genome Browser: Free software for distribution and exploration of genome-scale data sets. |journal=Bioinformatics |volume=25 |issue=20 |pages=2730–2731|year=2009 |pmid=19654113 |pmc=2759552 |doi=10.1093/bioinformatics/btp472}}</ref>
|-
! [[Jalview]]
|a multiple alignment editor written in Java.
||yes||no|| [http://www.jalview.org/ sourcecode] || <ref name="pmid19151095">{{cite journal |author=Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ |title=Jalview Version 2--a multiple sequence alignment editor and analysis workbench. |journal=Bioinformatics |volume=25 |issue=9 |pages=1189–91 |year=2009 |pmid=19151095 |doi=10.1093/bioinformatics/btp033 |pmc=2672624}}</ref><ref name="pmid14960472">{{cite journal |author=Clamp M, Cuff J, Searle SM, Barton GJ |title=The Jalview Java alignment editor. |journal=Bioinformatics |volume=20 |issue=3 |pages=426–7 |year=2004 |pmid=14960472 |doi=10.1093/bioinformatics/btg430}}</ref>
|-
! [[RALEE]]
|a major mode for the [[Emacs]] text editor. It provides functionality to aid the viewing and editing of multiple sequence alignments of structured RNAs.||yes||yes || [http://personalpages.manchester.ac.uk/staff/sam.griffiths-jones/software/ralee/ sourcecode] || <ref name="pmid15377506">{{cite journal | author = Griffiths-Jones S | title = RALEE--RNA ALignment editor in Emacs | journal = Bioinformatics | volume = 21 | issue = 2 | pages = 257–9 | year = 2005 | pmid = 15377506 | doi = 10.1093/bioinformatics/bth489 }}</ref>
|-
! [[SARSE]]
|A graphical sequence editor for working with structural alignments of RNA.||yes||yes|| [http://sarse.kvl.dk/ sourcecode]|| <ref name="pmid17804647">{{cite journal | author = Andersen ES, Lind-Thomsen A, Knudsen B, ''et al.'' | title = Semiautomated improvement of RNA alignments | journal = RNA | volume = 13 | issue = 11 | pages = 1850–9 | year = 2007 | pmid = 17804647 | doi = 10.1261/rna.215407 | pmc = 2040093 }}</ref>
|-
| colspan=6|
;Notes:{{reflist|group=Note}}
|}
 
==Inverse Folding/RNA design==
{| class="wikitable sortable"
! Name
! Description || Link || References
|-
! [[ETeRNA]]
|An RNA folding game that challenges players to come up with sequences that fold into a target RNA structure. The best sequences for a given puzzle are synthesized and their structures are probed through chemical mapping. The sequences are then scored by the data's agreement to the target structure and feedback is provided to the players. || [http://eterna.cmu.edu/content/EteRNA home page] || --
|-
! [[NUPACK]]
| Although NUPACK can be used to get useful statistics and properties of an RNA's structure as mentioned above, its main goal is design of new sequences that fold into a desired structure.|| [http://nupack.org/ home page] || <ref name="NUPACK">{{cite journal | doi=10.1137/060651100 | author = R.M. Dirks, J.S. Bois, J.M. Schaeffer, E. Winfree, N.A. Pierce | title = Thermodynamic Analysis of Interacting Nucleic Acid Strands | journal =  SIAM Review | volume = 49 | issue=1  | pages = 65–88 | year = 2007|bibcode = 2007SIAMR..49...65D }}</ref>
|-
! [[RNAInverse]]
| The ViennaRNA package provides RNAInverse, an algorithm for designing sequences with desired structure.|| [http://www.tbi.univie.ac.at/~ivo/RNA/man/RNAinverse.html help page] || <ref name="RNAInverse">{{cite journal | author = I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster | title = Fast Folding and Comparison of RNA Secondary Structures. | journal =  Monatshefte f. Chemie | volume = 125 | issue = 2 | pages = 167–188 | year = 1994 | doi = 10.1007/BF00818163}}</ref>
|-
! [[RNAiFold]]
| A complete RNA inverse folding approach based in [[constraint programming]] which allows for the specification of a wide range of design constraints.|| [http://bioinformatics.bc.edu/clotelab/RNAiFold/ home page] || <ref name="RNAiFold">{{cite journal | author = JA. Garcia-Martin, P. Clote, I. Dotu | title = RNAiFOLD: A CONSTRAINT PROGRAMMING ALGORITHM FOR RNA INVERSE FOLDING AND MOLECULAR DESIGN. | journal =  {Journal of Bioinformatics and Computational Biology | volume = 11 | issue = 02 | pages = 1350001 | year = 2013 | doi = 10.1142/S0219720013500017 | pmid = 23600819}}</ref>
|}
 
==Secondary structure viewers/editors==
{| class="wikitable sortable"
! Name
! Description || Link || References
|-
! PseudoViewer
|Automatically visualizing RNA pseudoknot structures as planar graphs. || [http://wilab.inha.ac.kr/pseudoviewer/ webapp/binary] || <ref name="pmid19369500">{{cite journal |author=Byun Y, Han K |title=PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots. |journal=Bioinformatics |volume=25 |issue=11 |pages=1435–7 |year=2009 |pmid=19369500 |doi=10.1093/bioinformatics/btp252}}</ref><ref name="pmid16845039">{{cite journal |author=Byun Y, Han K |title=PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures. |journal=Nucleic Acids Res |volume=34 |issue=Web Server issue |pages=W416–22 |year=2006 |pmid=16845039 |doi=10.1093/nar/gkl210 |pmc=1538805}}</ref><ref name="pmid12824341">{{cite journal |doi=10.1093/nar/gkg539 |author=Han K, Byun Y |title=PSEUDOVIEWER2: Visualization of RNA pseudoknots of any type. |journal=Nucleic Acids Res |volume=31 |issue=13 |pages=3432–40 |year=2003 |pmid=12824341 |pmc=168946}}</ref><ref name="pmid12169562">{{cite journal |author=Han K, Lee Y, Kim W |title=PseudoViewer: automatic visualization of RNA pseudoknots. |series=18 |journal=Bioinformatics |volume=Suppl 1 |issue= |pages=S321–8 |year=2002 |pmid=12169562 | doi = 10.1093/bioinformatics/18.suppl_1.S321 }}</ref>
|-
! RNA Movies
|browse sequential paths through RNA secondary structure landscapes || [http://bibiserv.techfak.uni-bielefeld.de/rnamovies sourcecode] || <ref name="pmid17567618">{{cite journal |author=Kaiser A, Krüger J, Evers DJ |title=RNA Movies 2: sequential animation of RNA secondary structures. |journal=Nucleic Acids Res |volume=35 |issue=Web Server issue |pages=W330–4 |year=2007 |pmid=17567618 |doi=10.1093/nar/gkm309 |pmc=1933240}}</ref><ref name="pmid10068690">{{cite journal |doi=10.1093/bioinformatics/15.1.32 |author=Evers D, Giegerich R |title=RNA movies: visualizing RNA secondary structure spaces. |journal=Bioinformatics |volume=15 |issue=1 |pages=32–7 |year=1999 |pmid=10068690}}</ref>
|-
! RNA2D3D
|a program for generating, viewing, and comparing 3-dimensional models of RNA || [http://www-lmmb.ncifcrf.gov/~bshapiro/software.html binary] || <ref name="pmid18399701">{{cite journal |author=Martinez HM, Maizel JV, Shapiro BA |title=RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA. |journal=J Biomol Struct Dyn |volume=25 |issue=6 |pages=669–83 |year=2008 |pmid=18399701}}</ref>
|-
! RNAstructure
|RNAstructure has a viewer for structures in ct files.  It can also compare predicted structures using the circleplot program.  Structures can be output as postscript files. || [http://rna.urmc.rochester.edu/RNAstructure.html sourcecode] || <ref name="pmid20230624 ">{{cite journal |author=Reuter JS, Mathews DH |title=RNAstructure: software for RNA secondary structure prediction and analysis. |journal=BMC Bioinformatics |volume=11 |pages=129 |year=2010 |pmid=20230624|doi = 10.1186/1471-2105-11-129 |pmc=2984261}}</ref>
|-
! RNAView/RnamlView
|Use RNAView to automatically identify and classify the types of base pairs that are formed in nucleic acid structures. Use RnamlView to arrange RNA structures. || [http://ndbserver.rutgers.edu/services/ sourcecode] || <ref name="pmid12824344">{{cite journal |doi=10.1093/nar/gkg529 |author=Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H, Westhof E |title=Tools for the automatic identification and classification of RNA base pairs. |journal=Nucleic Acids Res |volume=31 |issue=13 |pages=3450–60 |year=2003 |pmid=12824344 |pmc=168936}}</ref>
|-
! RILogo
|Visualizes the intra-/intermolecular base pairing of two interacting RNAs with sequence logos in a planar graph. || [http://rth.dk/resources/rilogo web server / sourcecode] || <ref name="pmid22826541">{{cite journal |doi=10.1093/bioinformatics/bts461 |author=Menzel P, Seemann SE, Gorodkin J |title=RILogo: visualizing RNA-RNA interactions. |journal=Bioinformatics |volume=28 |issue=19 |pages=2523–6 |year=2012 |pmid=22826541}}</ref>
|-
! VARNA
|A tool for the automated drawing, visualization and annotation of the secondary structure of RNA, initially designed as a companion software for web servers and databases || [http://varna.lri.fr webapp/sourcecode] || <ref name="pmid19398448">{{cite journal |author=Darty K, Denise A, Ponty Y |title=VARNA: Interactive drawing and editing of the RNA secondary structure. |journal=Bioinformatics |volume=25 |issue=15 |pages=1974–5 |year=2009 |pmid=19398448 |doi=10.1093/bioinformatics/btp250 |pmc=2712331}}</ref>
|}
 
==See also==
* [[RNA]]
* [[Non-coding RNA]]
* [[RNA structure]]
* [[List of nucleic acid simulation software]]
 
==References==
{{reflist|2}}
 
{{DEFAULTSORT:List Of Rna Structure Prediction Software}}
[[Category:Bioinformatics software]]
[[Category:Lists of software|RNA structure prediction software]]
[[Category:RNA]]

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