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|'''4sale'''
|'''4sale'''
|A tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing||yes||yes|| [http://4sale.bioapps.biozentrum.uni-wuerzburg.de/index.html source]||
|A tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing||yes||yes || [http://4sale.bioapps.biozentrum.uni-wuerzburg.de/index.html source] || <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 | issue = | pages = 498 | year = 2006 | pmid = 17101042 | doi = 10.1186/1471-2105-7-498 | issn = }}</ref>
|-
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|'''RALEE'''
|'''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]||
|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 | issn = }}</ref>
|-
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|'''SARSE'''
|'''SARSE'''
|A graphical sequence editor for working with structural alignments of RNA.||yes||yes|| [http://sarse.kvl.dk/ sourcecode]||
|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 | issn = }}</ref>
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|colspan="7" | <small><nowiki>*</nowiki> '''Alignment:''' view and edit an [[sequence alignment|alignment,]] <yes|no>. <nowiki>*</nowiki> '''Structure:''' view and edit [[RNA structure|structure,]] <yes|no></small>
|colspan="7" | <small><nowiki>*</nowiki> '''Alignment:''' view and edit an [[sequence alignment|alignment,]] <yes|no>. <nowiki>*</nowiki> '''Structure:''' view and edit [[RNA structure|structure,]] <yes|no></small>

Revision as of 19:09, 20 January 2008

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

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 [1]
KineFold Folding kinetics of RNA sequences including pseudoknots. yes linuxbinary, webserver [2][3]
Mfold MFE RNA structure prediction algorithm. no sourcecode, webserver [4]
Pknots A dynamic programming algorithm for optimal RNA pseudoknot prediction using the nearest neighbour energy model. yes sourcecode [5]
PknotsRG A dynamic programming algorithm for the prediction of a restricted class of RNA pseudoknots. yes sourcecode, webserver [6]
RNAfold MFE RNA structure prediction algorithm. Includes an implementation of the partition function for computing basepair probabilities and circular RNA folding. no sourcecode, webserver

[7] [4][8][9][10][11]

Sfold Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities. no webserver [12][13][14][15]
*Knots: Pseudoknot prediction, <yes|no>.


Comparative methods

Name Description Number of sequences Alignment Structure Knots Link References
Carnac Comparative analysis combined with MFE folding. any no yes no sourcecode, webserver [16][17]
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. yes yes no sourcecode, webserver [18]
CONSAN implements a pinned Sankoff algorithm for simultaneous pairwise RNA alignment and consensus structure prediction. 2 yes yes no sourcecode [19]
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 [20] [21] [22]
FoldalignM A multiple RNA structural RNA alignment method, to a large extend based on the PMcomp program. any yes yes no sourcecode [23]
KNetFold Computes a consensus RNA secondary structure from an RNA sequence alignment based on machine learning. any input yes yes linuxbinary, webserver [24]
LARA Produce a global fold and alignment of ncRNA families using integer linear programming and Lagrangian relaxation. any yes yes no sourcecode [25]
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 [26] [27]
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 [28]
Pfold Folds alignments using a SCFG trained on rRNA alignments. input yes no webserver [29][30]
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 yes yes no sourcecode, webserver [31]
RNAalifold Folds precomputed alignments using a combination of free-energy and a covariation measures. Ships with the Vienna package. any input yes no link [7] [32]
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 [33]
RNAforester Compare and align RNA secondary structures via a "forest alignment" approach. any yes input no sourcecode, webserver [34] [35]
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 [36]
RNASampler a probabilistic sampling approach and combines intrasequence base pairing probabilities and intersequence base alignment probabilities to prediction consensus structure on two sequences. It is extended by using a consistency-based method to incorporates pairwise structural information to predict the common structure conserved among multiple sequences. any yes yes yes sourcecode [37]
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 [38]
SimulFold simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. any yes yes yes sourcecode [39]
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 [40]
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. yes no no sourcecode, webserver [41]
* Number of sequences: <any|num>. * Alignment: predicts an alignment, <input|yes|no>. * Structure: predicts structure, <input|yes|no>. * Knots: pseudoknot prediction, <yes|no>.

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 of rRNA, U4 spliceosomal RNA and U6 spliceosomal RNA form a complex and many small bacterial RNAs regulate gene expression by antisense interactions.

Name Description miRNA specific Intra-molecular structure Comparative Link References
RNAaliduplex Based upon RNAduplex with bonuses for covarying sites no no yes sourcecode [7]
RNAcofold works much like RNAfold, but allows to specify two RNA sequences wich are then allowed to form a dimer structure. no yes no sourcecode [7] [42]
RNAduplex computes optimal and suboptimal secondary structures for hybridization. The calculation is simplified by allowing only inter-molecular base pairs. no no no sourcecode [7]
RNAhybrid a tool for finding the minimum free energy hybridisation of a long and a short RNA. yes no no sourcecode, webserver [43] [44]
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 [7] [45]
* Number of sequences: <any|num>. * Alignment: predicts an alignment, <input|yes|no>. * Structure: predicts structure, <input|yes|no>. * Knots: pseudoknot prediction, <yes|no>.

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 [46]
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 [47]
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 [48] [49]
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 [50] [51] [52]
* Number of sequences: <any|num>. * Alignment: predicts an alignment, <input|yes|no>. * Structure: predicts structure, <input|yes|no>.

Benchmarks

Name Description Structure Alignment Phylogeny Links References
BRalibase I A comprehensive comparison of comparative RNA structure prediction approaches yes no no data
BRalibase II A benchmark of multiple sequence alignment programs upon structural RNAs no yes no data
BRalibase III A critical assessment of the performance of homology search methods on noncoding RNA no yes no data [53]
* Alignment: benchmarks alignment tools <yes|no>. * Structure: benchmarks structure prediction tools <yes|no>.


Viewers/Editors

Name Description Alignment Structure Link References
4sale A tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing yes yes source [54]
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 [55]
SARSE A graphical sequence editor for working with structural alignments of RNA. yes yes sourcecode [56]
* Alignment: view and edit an alignment, <yes|no>. * Structure: view and edit structure, <yes|no>

References

  1. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ a b 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.
  5. ^ 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.
  6. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  7. ^ a b c d e f 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  8. ^ 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.
  9. ^ 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.
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  11. ^ Douglas Adams. The Hitchhiker's Guide to the Galaxy. ISBN 0-330-25864-8. {{cite book}}: Unknown parameter |published= ignored (help)
  12. ^ Ding Y, Lawrence CE (2003). "A statistical sampling algorithm for RNA secondary structure prediction". Nucleic Acids Res. 31 (24): 7280–301. PMID 14654704.
  13. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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  17. ^ Touzet H, Perriquet O. (2004 Jul 1;). "CARNAC: folding families of related RNAs". Nucleic Acids Res. 32(Web Server issue): W142-5. PMID 15215367. {{cite journal}}: Check date values in: |year= (help)CS1 maint: extra punctuation (link)
  18. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  19. ^ 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  20. ^ 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.
  21. ^ 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.
  22. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  23. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  24. ^ 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.
  25. ^ Bauer M, Klau GW, Reinert K. (2007). "Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization". BMC Bioinformatics. 8 (271). PMID 17662141.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  26. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  27. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  28. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  29. ^ Knudsen B, Hein J (1999). "RNA secondary structure prediction using stochastic context-free grammars and evolutionary history". Bioinformatics. 15 (6): 446–54. PMID 10383470.
  30. ^ Knudsen B, Hein J (2003). "Pfold: RNA secondary structure prediction using stochastic context-free grammars". Nucleic Acids Res. 31 (13): 3423–8. PMID 12824339.
  31. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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  35. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  36. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  37. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  38. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  39. ^ 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
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  41. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  42. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  43. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  44. ^ 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.
  45. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  46. ^ 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.
  47. ^ 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. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  48. ^ Rivas E, Eddy SR (2001). "Noncoding RNA gene detection using comparative sequence analysis". BMC Bioinformatics. 2: 8. PMID 11801179.
  49. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  50. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  51. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  52. ^ Washietl S (2007). "Prediction of Structural Noncoding RNAs With RNAz". Methods Mol. Biol. 395: 503–26. PMID 17993695.
  53. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  54. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  55. ^ Griffiths-Jones S (2005). "RALEE--RNA ALignment editor in Emacs". Bioinformatics. 21 (2): 257–9. doi:10.1093/bioinformatics/bth489. PMID 15377506.
  56. ^ 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. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
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