List of RNA structure prediction software

From DrugPedia: A Wikipedia for Drug discovery

This list of RNA structure prediction software is a compilation of software tools and web portals used for RNA structure prediction.

Contents 1 Single sequence structure prediction 2 Comparative methods 3 Inter molecular interactions: RNA-RNA 4 ncRNA gene prediction software 5 Benchmarks 6 Viewers/Editors 7 See also 8 References

[edit] Single sequence structure prediction

Name	Description	Knots	Links	References
CONTRAfold	Secondary structure prediction method based on conditional log-linear models (CLLMs), a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring.	no	sourcecode webserver	<ref name="pmid16873527">Do CB, Woods DA, Batzoglou S (2006). "CONTRAfold: RNA secondary structure prediction without physics-based models". Bioinformatics 22 (14): e90–8. doi:10.1093/bioinformatics/btl246. PMID 16873527. </ref>
KineFold	Folding kinetics of RNA sequences including pseudoknots.	yes	linuxbinary, webserver	<ref name="pmid15980546">Xayaphoummine A, Bucher T, Isambert H (2005). "Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots". Nucleic Acids Res. 33 (Web Server issue): W605–10. doi:10.1093/nar/gki447. PMID 15980546. </ref><ref name="pmid14676318">Xayaphoummine A, Bucher T, Thalmann F, Isambert H (2003). "Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations". Proc. Natl. Acad. Sci. U.S.A. 100 (26): 15310–5. doi:10.1073/pnas.2536430100. PMID 14676318. </ref>
Mfold	MFE RNA structure prediction algorithm.	no	sourcecode, webserver	<ref name="pmid6163133">Zuker M, Stiegler P (1981). "Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information". Nucleic Acids Res. 9 (1): 133–48. PMID 6163133. </ref>
Pknots	A dynamic programming algorithm for optimal RNA pseudoknot prediction using the nearest neighbour energy model.	yes	sourcecode	<ref name="pmid9925784">Rivas E, Eddy SR (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". J. Mol. Biol. 285 (5): 2053–68. doi:10.1006/jmbi.1998.2436. PMID 9925784. </ref>
PknotsRG	A dynamic programming algorithm for the prediction of a restricted class of RNA pseudoknots.	yes	sourcecode, webserver	<ref name="pmid17478505">Reeder J, Steffen P, Giegerich R (2007). "pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows". Nucleic Acids Res. 35 (Web Server issue): W320–4. doi:10.1093/nar/gkm258. PMID 17478505. </ref>
RNAfold	MFE RNA structure prediction algorithm. Includes an implementation of the partition function for computing basepair probabilities and circular RNA folding.	no	sourcecode, webserver	<ref name="vienna rna">I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994). "Fast Folding and Comparison of RNA Secondary Structures.". Monatshefte f. Chemie 125: 167–188. doi:10.1007/BF00818163. </ref> <ref name="pmid6163133">Zuker M, Stiegler P (1981). "Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information". Nucleic Acids Res. 9 (1): 133–48. PMID 6163133. </ref><ref name="pmid1695107">McCaskill JS (1990). "The equilibrium partition function and base pair binding probabilities for RNA secondary structure". Biopolymers 29 (6-7): 1105–19. doi:10.1002/bip.360290621. PMID 1695107. </ref><ref name="pmid16452114">Hofacker IL, Stadler PF (2006). "Memory efficient folding algorithms for circular RNA secondary structures". Bioinformatics 22 (10): 1172–6. doi:10.1093/bioinformatics/btl023. PMID 16452114. </ref><ref name="pmid17611759">Bompfünewerer AF, Backofen R, Bernhart SH, et al (2008). "Variations on RNA folding and alignment: lessons from Benasque". J Math Biol 56 (1-2): 129–144. doi:10.1007/s00285-007-0107-5. PMID 17611759. </ref><ref name="book1">Template:Cite book</ref>
Sfold	Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities.	no	webserver	<ref name="pmid14654704">Ding Y, Lawrence CE (2003). "A statistical sampling algorithm for RNA secondary structure prediction". Nucleic Acids Res. 31 (24): 7280–301. PMID 14654704. </ref><ref name="pmid15215366">Ding Y, Chan CY, Lawrence CE (2004). "Sfold web server for statistical folding and rational design of nucleic acids". Nucleic Acids Res. 32 (Web Server issue): W135–41. doi:10.1093/nar/gkh449. PMID 15215366. </ref><ref name="pmid16043502">Ding Y, Chan CY, Lawrence CE (2005). "RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble". RNA 11 (8): 1157–66. doi:10.1261/rna.2500605. PMID 16043502. </ref><ref name="pmid16109749">Chan CY, Lawrence CE, Ding Y (2005). "Structure clustering features on the Sfold Web server". Bioinformatics 21 (20): 3926–8. doi:10.1093/bioinformatics/bti632. PMID 16109749. </ref>
*Knots: Pseudoknot prediction, <yes|no>.

[edit] 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.

Name	Description	Number of sequences	Alignment	Structure	Knots	Link	References
Carnac	Comparative analysis combined with MFE folding.	any	no	yes	no	sourcecode, webserver	<ref name="pmid12499300">Perriquet O, Touzet H, Dauchet M. (2003). "Finding the common structure shared by two homologous RNAs.". Bioinformatics. 19 (1): 108–16. doi:10.1093/bioinformatics/19.1.108. PMID 12499300. </ref><ref name="pmid15215367">Touzet H, Perriquet O. (2004 Jul 1;). "CARNAC: folding families of related RNAs.". Nucleic Acids Res. 32 (Web Server issue): W142–5.. PMID 15215367. </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>4\le seqs \le60</math>	yes	yes	no	sourcecode, webserver	<ref name="pmid16357030">Yao Z, Weinberg Z, Ruzzo WL (2006). "CMfinder--a covariance model based RNA motif finding algorithm". Bioinformatics 22 (4): 445–52. doi:10.1093/bioinformatics/btk008. PMID 16357030. </ref>
CONSAN	implements a pinned Sankoff algorithm for simultaneous pairwise RNA alignment and consensus structure prediction.	2	yes	yes	no	sourcecode	<ref name="pmid16952317">Dowell RD, Eddy SR (2006). "Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints". BMC Bioinformatics 7: 400. doi:10.1186/1471-2105-7-400. PMID 16952317. </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	sourcecode	<ref name="pmid11902836">Mathews DH, Turner DH (2002). "Dynalign: an algorithm for finding the secondary structure common to two RNA sequences". J. Mol. Biol. 317 (2): 191–203. doi:10.1006/jmbi.2001.5351. PMID 11902836. </ref> <ref name="pmid15731207">Mathews DH (2005). "Predicting a set of minimal free energy RNA secondary structures common to two sequences". Bioinformatics 21 (10): 2246–53. doi:10.1093/bioinformatics/bti349. PMID 15731207. </ref> <ref name="pmid17445273">Harmanci AO, Sharma G, Mathews DH (2007). "Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign". BMC Bioinformatics 8: 130. doi:10.1186/1471-2105-8-130. PMID 17445273. </ref>
FoldalignM	A multiple RNA structural RNA alignment method, to a large extend based on the PMcomp program.	any	yes	yes	no	sourcecode	<ref name="pmid17324941">Torarinsson E, Havgaard JH, Gorodkin J (2007). "Multiple structural alignment and clustering of RNA sequences". Bioinformatics 23 (8): 926–32. doi:10.1093/bioinformatics/btm049. PMID 17324941. </ref>
KNetFold	Computes a consensus RNA secondary structure from an RNA sequence alignment based on machine learning.	any	input	yes	yes	linuxbinary, webserver	<ref name="pmid16495232">Bindewald E, Shapiro BA (2006). "RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers". RNA 12 (3): 342–52. doi:10.1261/rna.2164906. PMID 16495232. </ref>
LARA	Produce a global fold and alignment of ncRNA families using integer linear programming and Lagrangian relaxation.	any	yes	yes	no	sourcecode	<ref name="pmid17662141">Bauer M, Klau GW, Reinert K. (2007). "Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.". BMC Bioinformatics. 8 (271): 271. doi:10.1186/1471-2105-8-271. PMID 17662141. </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	sourcecode	<ref name="pmid17432929">Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R (20047). "Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.". PLoS Comput Biol. 3 (4): e65. doi:10.1371/journal.pcbi.0030065. PMID 17432929. </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	sourcecode	<ref name="pmid17038338">Lindgreen S, Gardner PP, Krogh A (2006). "Measuring covariation in RNA alignments: physical realism improves information measures". Bioinformatics 22 (24): 2988–95. doi:10.1093/bioinformatics/btl514. PMID 17038338. </ref> <ref name="pmid18006551">Lindgreen S, Gardner PP, Krogh A (2007). "MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing". Bioinformatics 23 (24): 3304–11. doi:10.1093/bioinformatics/btm525. PMID 18006551. </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	webserver	<ref name="pmid17459961">Kiryu H, Tabei Y, Kin T, Asai K (2007). "Murlet: a practical multiple alignment tool for structural RNA sequences". Bioinformatics 23 (13): 1588–98. doi:10.1093/bioinformatics/btm146. PMID 17459961. </ref>
MXSCARNA	a multiple alignment tool for RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA.	any	yes	yes	no	webserver sourcecode	<ref name="MXSCARNA">Tabei Y, Kiryu H, Kin T, Asai K (2008). "A fast structural multiple alignment method for long RNA sequences". BMC Bioinformatics 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	sourcecode	<ref name="pmid18304945">Harmanci AO, Sharma G, Mathews DH (2008). "PARTS: probabilistic alignment for RNA joinT secondary structure prediction.". Nucleic Acids Res 36 (7): 2406–17. doi:10.1093/nar/gkn043. PMID 18304945. </ref>
Pfold	Folds alignments using a SCFG trained on rRNA alignments.	<math>\le40</math>	input	yes	no	webserver	<ref name="pmid10383470">Knudsen B, Hein J (1999). "RNA secondary structure prediction using stochastic context-free grammars and evolutionary history". Bioinformatics 15 (6): 446–54. PMID 10383470. </ref><ref name="pmid12824339">Knudsen B, Hein J (2003). "Pfold: RNA secondary structure prediction using stochastic context-free grammars". Nucleic Acids Res. 31 (13): 3423–8. PMID 12824339. </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	sourcecode, webserver	<ref name="pmid15073017">Hofacker IL, Bernhart SH, Stadler PF (2004). "Alignment of RNA base pairing probability matrices". Bioinformatics 20 (14): 2222–7. doi:10.1093/bioinformatics/bth229. PMID 15073017. </ref>
RNAalifold	Folds precomputed alignments using a combination of free-energy and a covariation measures. Ships with the Vienna package.	any	input	yes	no	link	<ref name="vienna rna">I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994). "Fast Folding and Comparison of RNA Secondary Structures.". Monatshefte f. Chemie 125: 167–188. doi:10.1007/BF00818163. </ref> <ref name="pmid12079347">Hofacker IL, Fekete M, Stadler PF (2002). "Secondary structure prediction for aligned RNA sequences". J. Mol. Biol. 319 (5): 1059–66. doi:10.1016/S0022-2836(02)00308-X. PMID 12079347. </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	sourcecode, webserver	<ref name="pmid16020472">Reeder J, Giegerich R (2005). "Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction". Bioinformatics 21 (17): 3516–23. doi:10.1093/bioinformatics/bti577. PMID 16020472. </ref>
RNAforester	Compare and align RNA secondary structures via a "forest alignment" approach.	any	yes	input	no	sourcecode, webserver	<ref name="pmid16452790">Höchsmann M, Töller T, Giegerich R, Kurtz S (2003). "Local similarity in RNA secondary structures". Proc IEEE Comput Soc Bioinform Conf 2: 159–68. PMID 16452790. </ref> <ref name="pmid17048408">Höchsmann M, Voss B, Giegerich R (2004). "Pure multiple RNA secondary structure alignments: a progressive profile approach". IEEE/ACM Trans Comput Biol Bioinform 1 (1): 53–62. doi:10.1109/TCBB.2004.11. PMID 17048408. </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	webserver	<ref name="pmid16908501">Hamada M, Tsuda K, Kudo T, Kin T, Asai K (2006). "Mining frequent stem patterns from unaligned RNA sequences". Bioinformatics 22 (20): 2480–7. doi:10.1093/bioinformatics/btl431. PMID 16908501. </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	sourcecode	<ref name="pmid17537756">Xu X, Ji Y, Stormo GD (2007). "RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment". Bioinformatics 23 (15): 1883–91. doi:10.1093/bioinformatics/btm272. PMID 17537756. </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	webserver	<ref name="pmid16690634">Tabei Y, Tsuda K, Kin T, Asai K (2006). "SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments". Bioinformatics 22 (14): 1723–9. doi:10.1093/bioinformatics/btl177. PMID 16690634. </ref>
SimulFold	simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework.	any	yes	yes	yes	sourcecode	<ref name="pmid17696604">Meyer IM, Miklós I (2007). "SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework". PLoS Comput. Biol. 3 (8): e149. doi:10.1371/journal.pcbi.0030149. PMID 17696604. </ref>
Stemloc	a program for pairwise RNA structural alignment based on probabilistic models of RNA structure known as Pair stochastic context-free grammars.	any	yes	yes	no	sourcecode	<ref name="pmid15790387">Holmes I (2005). "Accelerated probabilistic inference of RNA structure evolution". BMC Bioinformatics 6: 73. doi:10.1186/1471-2105-6-73. PMID 15790387. </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	sourcecode, webserver	<ref name="pmid16613908">Dalli D, Wilm A, Mainz I, Steger G (2006). "STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time". Bioinformatics 22 (13): 1593–9. doi:10.1093/bioinformatics/btl142. PMID 16613908. </ref>
Xrate	a program for analysis of multiple sequence alignments using phylogenetic grammars, that may be viewed as a flexible generalization of the "Pfold" program.	any	yes	yes	no	sourcecode	<ref name="pmid17018148">Klosterman P (2006). "XRate: a fast prototyping, training and annotation tool for phylo-grammars". BMC Bioinformatics 3 (7): 428. doi:10.1186/1471-2105-7-428. PMID 17018148. </ref>
* Number of sequences: <any|num>. * Alignment: predicts an alignment, <input|yes|no>. * Structure: predicts structure, <input|yes|no>. * Knots: pseudoknot prediction, <yes|no>.

[edit] Inter molecular interactions: RNA-RNA

Many ncRNAs function by binding to other RNAs. For example, miRNAs regulate protein coding gene expression by binding to 3' UTRs, 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 Eg. GcvB, OxyS and RyhB.

Name	Description	miRNA specific	Intra-molecular structure	Comparative	Link	References
RNAaliduplex	Based upon RNAduplex with bonuses for covarying sites	no	no	yes	sourcecode	<ref name="vienna rna">I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994). "Fast Folding and Comparison of RNA Secondary Structures.". Monatshefte f. Chemie 125: 167–188. doi:10.1007/BF00818163. </ref>
RNAcofold	works much like RNAfold, but allows to specify two RNA sequences which are then allowed to form a dimer structure.	no	yes	no	sourcecode	<ref name="vienna rna">I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994). "Fast Folding and Comparison of RNA Secondary Structures.". Monatshefte f. Chemie 125: 167–188. doi:10.1007/BF00818163. </ref> <ref name="pmid16722605">Bernhart SH, Tafer H, Mückstein U, Flamm C, Stadler PF, Hofacker IL (2006). "Partition function and base pairing probabilities of RNA heterodimers". Algorithms Mol Biol 1 (1): 3. doi:10.1186/1748-7188-1-3. PMID 16722605. </ref>
RNAduplex	computes optimal and suboptimal secondary structures for hybridization. The calculation is simplified by allowing only inter-molecular base pairs.	no	no	no	sourcecode	<ref name="vienna rna">I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994). "Fast Folding and Comparison of RNA Secondary Structures.". Monatshefte f. Chemie 125: 167–188. doi:10.1007/BF00818163. </ref>
RNAhybrid	a tool for finding the minimum free energy hybridisation of a long and a short RNA.	yes	no	no	sourcecode, webserver	<ref name="pmid15383676">Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R (2004). "Fast and effective prediction of microRNA/target duplexes". RNA 10 (10): 1507–17. doi:10.1261/rna.5248604. PMID 15383676. </ref> <ref name="pmid16845047">Krüger J, Rehmsmeier M (2006). "RNAhybrid: microRNA target prediction easy, fast and flexible". Nucleic Acids Res. 34 (Web Server issue): W451–4. doi:10.1093/nar/gkl243. PMID 16845047. </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.	no	yes	no	sourcecode	<ref name="vienna rna">I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994). "Fast Folding and Comparison of RNA Secondary Structures.". Monatshefte f. Chemie 125: 167–188. doi:10.1007/BF00818163. </ref> <ref name="pmid16446276">Mückstein U, Tafer H, Hackermüller J, Bernhart SH, Stadler PF, Hofacker IL (2006). "Thermodynamics of RNA-RNA binding". Bioinformatics 22 (10): 1177–82. doi:10.1093/bioinformatics/btl024. PMID 16446276. </ref>
* Number of sequences: <any|num>. * Alignment: predicts an alignment, <input|yes|no>. * Structure: predicts structure, <input|yes|no>. * Knots: pseudoknot prediction, <yes|no>.

[edit] ncRNA gene prediction software

Name	Description	Number of sequences	Alignment	Structure	Link	References
Alifoldz	Assessing a multiple sequence alignment for the existence of an unusual stable and conserved RNA secondary structure.	any	input	yes	sourcecode	<ref name="pmid15313604">Washietl S, Hofacker IL (2004). "Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics". J. Mol. Biol. 342 (1): 19–30. doi:10.1016/j.jmb.2004.07.018. PMID 15313604. </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	linuxbinary	<ref name="pmid16628248">Pedersen JS, Bejerano G, Siepel A, et al (2006). "Identification and classification of conserved RNA secondary structures in the human genome". PLoS Comput. Biol. 2 (4): e33. doi:10.1371/journal.pcbi.0020033. PMID 16628248. </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	sourcecode	<ref name="pmid11801179">Rivas E, Eddy SR (2001). "Noncoding RNA gene detection using comparative sequence analysis". BMC Bioinformatics 2: 8. PMID 11801179. </ref> <ref name="pmid11553332">Rivas E, Klein RJ, Jones TA, Eddy SR (2001). "Computational identification of noncoding RNAs in E. coli by comparative genomics". Curr. Biol. 11 (17): 1369–73. PMID 11553332. </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	sourcecode, webserver	<ref name="pmid15665081">Washietl S, Hofacker IL, Stadler PF (2005). "Fast and reliable prediction of noncoding RNAs". Proc. Natl. Acad. Sci. U.S.A. 102 (7): 2454–9. doi:10.1073/pnas.0409169102. PMID 15665081. </ref> <ref name="pmid17452347">Gruber AR, Neuböck R, Hofacker IL, Washietl S (2007). "The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures". Nucleic Acids Res. 35 (Web Server issue): W335–8. doi:10.1093/nar/gkm222. PMID 17452347. </ref> <ref name="pmid17993695">Washietl S (2007). "Prediction of Structural Noncoding RNAs With RNAz". Methods Mol. Biol. 395: 503–26. PMID 17993695. </ref>
Xrate	a program for analysis of multiple sequence alignments using phylogenetic grammars, that may be viewed as a flexible generalization of the "Evofold" program.	any	yes	yes	sourcecode	<ref name="pmid17018148">Klosterman P (2006). "XRate: a fast prototyping, training and annotation tool for phylo-grammars". BMC Bioinformatics 3 (7): 428. doi:10.1186/1471-2105-7-428. PMID 17018148. </ref>
MSARi	heuristic search for statistically significant conservation of RNA secondary structure in deep multiple sequence alignments.	any	input	yes	sourcecode	<ref>Coventry A, Kleitman DJ, Berger BA (2004). "MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure". PNAS 101 (33): 12102–12107. doi:10.1073/pnas.0404193101. PMID 15304649. </ref>
* Number of sequences: <any|num>. * Alignment: predicts an alignment, <input|yes|no>. * Structure: predicts structure, <input|yes|no>.

[edit] Benchmarks

Name	Description	Structure	Alignment	Phylogeny	Links	References
BRalibase I	A comprehensive comparison of comparative RNA structure prediction approaches	yes	no	no	data	<ref name="pmid15458580">Gardner PP, Giegerich R (2004). "A comprehensive comparison of comparative RNA structure prediction approaches". BMC Bioinformatics 5: 140. doi:10.1186/1471-2105-5-140. PMID 15458580. </ref>
BRalibase II	A benchmark of multiple sequence alignment programs upon structural RNAs	no	yes	no	data	<ref name="pmid15860779">Gardner PP, Wilm A, Washietl S (2005). "A benchmark of multiple sequence alignment programs upon structural RNAs". Nucleic Acids Res. 33 (8): 2433–9. doi:10.1093/nar/gki541. PMID 15860779. </ref>
BRalibase III	A critical assessment of the performance of homology search methods on noncoding RNA	no	yes	no	data	<ref name="pmid17151342">Freyhult EK, Bollback JP, Gardner PP (2007). "Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA". Genome Res. 17 (1): 117–25. doi:10.1101/gr.5890907. PMID 17151342. </ref>
* Alignment: benchmarks alignment tools <yes|no>. * Structure: benchmarks structure prediction tools <yes|no>.

[edit] Viewers/Editors

Name	Description	Alignment	Structure	Link	References
4sale	A tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing	yes	yes	sourcecode	<ref name="pmid17101042">Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M (2006). "4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing". BMC Bioinformatics 7: 498. doi:10.1186/1471-2105-7-498. PMID 17101042. </ref>
Colorstock, SScolor, 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	sourcecode	<ref name="colorstock">Bendana YR, Holmes IH (2008). "Colorstock, SScolor, Rat ́on: RNA Alignment Visualization Tools". Bioinformatics. </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	sourcecode	<ref name="pmid15377506">Griffiths-Jones S (2005). "RALEE--RNA ALignment editor in Emacs". Bioinformatics 21 (2): 257–9. doi:10.1093/bioinformatics/bth489. PMID 15377506. </ref>
SARSE	A graphical sequence editor for working with structural alignments of RNA.	yes	yes	sourcecode	<ref name="pmid17804647">Andersen ES, Lind-Thomsen A, Knudsen B, et al (2007). "Semiautomated improvement of RNA alignments". RNA 13 (11): 1850–9. doi:10.1261/rna.215407. PMID 17804647. </ref>
* Alignment: view and edit an alignment, <yes|no>. * Structure: view and edit structure, <yes|no>

[edit] See also

• RNA
• Non-coding RNA
• RNA structure

[edit] References