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Primary DNA Sequence Databases

[edit]
Name Description Institution Links References
European Nucleotide Archive Secondary structure prediction based on generalized centroid estimator no sourcecode webserver [1]
GenBank 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 [2]
DNA Data Bank of Japan Secondary structure prediction method based on placement of helices allowing complex pseudoknots. yes webserver [3]
KineFold Folding kinetics of RNA sequences including pseudoknots by including an implementation of the partition function for knots. yes linuxbinary, webserver [4][5]
Mfold MFE RNA structure prediction algorithm. no sourcecode, webserver [6]
Pknots A dynamic programming algorithm for optimal RNA pseudoknot prediction using the nearest neighbour energy model. yes sourcecode [7]
PknotsRG A dynamic programming algorithm for the prediction of a restricted class of RNA pseudoknots. yes sourcecode, webserver [8]
RNAfold MFE RNA structure prediction algorithm. Includes an implementation of the partition function for computing basepair probabilities and circular RNA folding. no sourcecode, webserver

[6][9][10][11][12][13]

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 source & binaries, webserver [14][15]
RNAstructure A program to predict lowest free energy structures and base pair probabilities for RNA or DNA sequences. 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. no source & binaries

[16][17]

Sfold Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities. no webserver [18][19][20][21]
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 sourcecode [22]
*Knots: Pseudoknot prediction, <yes|no>.
  1. ^ Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai (2009). "Predictions of RNA secondary structure using generalized centroid estimators". Bioinformatics. 25 (4): 465–473. doi:10.1093/bioinformatics/btn601. PMID 16873527.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ 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)
  3. ^ Bindewald E, Kluth T, Shapiro BA (2010). "CyloFold: secondary structure prediction including pseudoknots". Nucleic Acids Research. Suppl (W): 368–72. doi:10.1093/nar/gkq432. PMID 20501603.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ 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. PMC 1160208. PMID 15980546.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ 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. PMC 307563. PMID 14676318.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ 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. doi:10.1093/nar/9.1.133. PMC 326673. PMID 6163133.
  7. ^ 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.
  8. ^ 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. PMC 1933184. PMID 17478505.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  9. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  10. ^ 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.
  11. ^ 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.
  12. ^ 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. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
  13. ^ Douglas Adams (1979). The Hitchhiker's Guide to the Galaxy. London: Pan Books. ISBN 0-330-25864-8. {{cite book}}: Unknown parameter |published= ignored (help)
  14. ^ R. Giegerich, B.Voß, M. Rehmsmeier (2004). "Abstract shapes of RNA". Nucleic Acids Res. 32 (16): 4843–4851. doi:10.1093/nar/gkh779. PMC 519098. PMID 15371549.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  15. ^ B. Voß, R. Giegerich, M. Rehmsmeier (2006). "Complete probabilistic analysis of RNA shapes". BMC Biology. 4 (5): 5. doi:10.1186/1741-7007-4-5. PMC 1479382. PMID 16480488.{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  16. ^ D.H. Mathews, M.D. Disney, J. L. Childs, S.J. Schroeder, M. Zuker, D.H. Turner (2004). "Incorporating chemical modification constraints into a dynamic programming algorothm for prediction of RNA secondary structure". Proceedings of the National Academy of Sciences, USA. 101 (19): 7287–7292. doi:10.1073/pnas.0401799101. PMC 409911. PMID 15123812.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  17. ^ D.H. Mathews (2004). "Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization". RNA. 10 (8): 1178–1190. doi:10.1261/rna.7650904. PMC 1370608. PMID 15272118.
  18. ^ Ding Y, Lawrence CE (2003). "A statistical sampling algorithm for RNA secondary structure prediction". Nucleic Acids Res. 31 (24): 7280–301. doi:10.1093/nar/gkg938. PMC 297010. PMID 14654704.
  19. ^ 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. PMC 441587. PMID 15215366.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  20. ^ 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. PMC 1370799. PMID 16043502.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  21. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  22. ^ Markham NR, Zuker M (2008). "UNAFold: software for nucleic acid folding and hybridization". Methods Mol Biol. 453: 3–31. doi:10.1007/978-1-60327-429-6_1. PMID 18712296.
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