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Sfold

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Original author(s)Ye Ding and Charles E. Lawrence
Developer(s)Dang Long and Chaochun Liu (application modeling); Clarence Chan, Adam Wolenc, William A. Rennie and Charles S. Carmack (software development)
Initial release1 April 2003; 21 years ago (2003-04-01)
Repositorygithub.com/Ding-RNA-Lab/Sfold
Operating systemLinux
Websitewww.healthresearch.org/sfold-software-for-sirna/

Sfold is a software program developed to predict probable RNA secondary structures through structure ensemble sampling and centroid predictions[1][2] with a focus on assessment of RNA target accessibility,[3] for major applications to the rational design of siRNAs[4] in the suppression of gene expressions, and to the identification of targets for regulatory RNAs particularly microRNAs.[5][6]

Development

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The core RNA secondary structure prediction algorithm is based on rigorous statistical (stochastic) sampling of Boltzmann ensemble of RNA secondary structures, enabling statistical characterization of any local structural features of potential interest to experimental investigators. In a review on nucleic acid structure and prediction,[7] the potential of structure sampling described in a prototype algorithm[8] was highlighted. With the publication of the mature algorithms for Sfold,[1][2] the sampling approach became the focus of a review[9] Both the sampling approach and the centroid predictions were discussed in a comprehensive review.[10] As an application module of the Sfold package, the STarMir program[11] has been widely used for its capability in modeling target accessibility.[6] STarMir was described in an independent study on microRNA target prediction[12] STarMir predictions have been used in an attempt to derive improved predictions.[13] Predictions by Sfold have led to new biological insights.[14] The novel ideas of ensemble sampling and centroids have been adopted by others not only for RNA problems, but also for other fundamental problems in computational biology and genomics.[15][16][17][18][19]

An implementation of stochastic sampling has been included in two widely used RNA software packages, RNA Structure[20] and the ViennaRNA Package,[21] which are also based on the Turner RNA thermodynamic parameters.[22] Sfold was featured on a Nucleic Acids Research cover,[23] and was highlighted in Science NetWatch.[24] The underlying novel model for STarMir[11] was featured in the Cell Biology section of Nature Research Highlights.[25]

Distribution

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Sfold runs on Linux, and is freely available to the scientific community for non-commercial applications, and is available under license for commercial applications. Both the source code and the executables are available at GitHub.

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References

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  1. ^ a b Ding, Y; Lawrence, CE (2003). "A statistical sampling algorithm for RNA secondary structure prediction". Nucleic Acids Res. 15, 31 (24): 7280–301. doi:10.1093/nar/gkg938. PMC 297010. PMID 14654704.
  2. ^ a b Ding, Y; Chan, CY; Lawrence, CE (2005). "RNA secondary structure prediction by centroids in a Bolzmann weighed ensemble". RNA. 11 (8): 1157–1166. doi:10.1261/rna.2500605. PMC 1370799. PMID 16043502.
  3. ^ Ding, Y; Lawrence, CE (2001). "Statistical Prediction of single stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond". Nucleic Acids Research. 1, 29 (5): 1035–46. doi:10.1093/nar/29.5.1034. PMC 29728. PMID 11222752.
  4. ^ Elbashir, SM; Harborth, J; Lendeckel, W; Yalcin, A; Weber, K; Tuschi, T (2001). ""Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells". Nature. 411 (6836): 494–8. doi:10.1038/35078107. PMID 11373684. S2CID 710341.
  5. ^ Lee, RC; Feinbaum, RL; Ambros, V (1993). "The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14". Cell. 75 (5): 843–54. doi:10.1016/0092-8674(93)90529-y. PMID 8252621. S2CID 205020975.
  6. ^ a b Long, D; Lee, R; William, P; Chan, CY; Ambros, V; Ding, Y (2007). "Potent effect of target secondary structure on microRNA function". Nat Struct Mol Biol. 14 (4): 287–94. doi:10.1038/nsmb1226. PMID 17401373. S2CID 650349.
  7. ^ Zucker, M. (2000). "Calculating nucleic acid secondary structure". Curr. Opin. Struct. Biol. 10 (3): 303–310. doi:10.1016/s0959-440x(00)00088-9. PMID 10851192.
  8. ^ Ding, Y.; Lawrence, C. E. (1999). "A Bayesian Statistical Algorithm for RNA Secondary Structure Prediction". Computers & Chemistry. 23 (3–4): 387–400. doi:10.1016/S0097-8485(99)00010-8. PMID 10404626.
  9. ^ Mathews, David H. (2006). "Revolutions in RNA Secondary Structure Prediction". Journal of Molecular Biology. 359 (3): 526–532. doi:10.1016/j.jmb.2006.01.067. ISSN 0022-2836. PMID 16500677.
  10. ^ Seetin, Matthew G.; Mathews, David H. (2012), "RNA Structure Prediction: An Overview of Methods", Bacterial Regulatory RNA, Methods in Molecular Biology, vol. 905, Totowa, NJ: Humana Press, pp. 99–122, doi:10.1007/978-1-61779-949-5_8, ISBN 978-1-61779-948-8, PMID 22736001, retrieved 2023-12-05
  11. ^ a b Rennie, William; Liu, Chaochun; Carmack, C. Steven; Wolenc, Adam; Kanoria, Shaveta; Lu, Jun; Long, Dang; Ding, Ye (2014-05-06). "STarMir: a web server for prediction of microRNA binding sites". Nucleic Acids Research. 42 (W1): W114–W118. doi:10.1093/nar/gku376. ISSN 1362-4962. PMC 4086099. PMID 24803672.
  12. ^ Wong, Leon; You, Zhu-Hong; Guo, Zhen-Hao; Yi, Hai-Cheng; Chen, Zhan-Heng; Cao, Mei-Yuan (2020-07-09). "MIPDH: A Novel Computational Model for Predicting microRNA–mRNA Interactions by DeepWalk on a Heterogeneous Network". ACS Omega. 5 (28): 17022–17032. doi:10.1021/acsomega.9b04195. ISSN 2470-1343. PMC 7376568. PMID 32715187.
  13. ^ Ullah, Abu Z.M. Dayem; Sahoo, Sudhakar; Steinhöfel, Kathleen; Albrecht, Andreas A. (2012). "Derivative scores from site accessibility and ranking of miRNA target predictions". International Journal of Bioinformatics Research and Applications. 8 (3/4): 171–191. doi:10.1504/ijbra.2012.048966. ISSN 1744-5485. PMID 22961450.
  14. ^ Adams, L. (2017). "Pri-miRNA processing: structure is the key". Nature Reviews Genetics. 18 (3): 145. doi:10.1038/nrg.2017.6. PMID 28138147. S2CID 30513706.
  15. ^ Huang, F. W.; Qin, Jing; Reidys, Christian M; Stadler, Peter F (2009). "Target prediction and a statistical sampling algorithm for RNA-RNA interaction". Bioinformatics. 26 (2): 175–181. doi:10.1093/bioinformatics/btp635. PMC 2804298. PMID 19910305.
  16. ^ Harmanchi, Arif Ozgun; Gaurav, Sharma; Mathews, David H (2009). "Stochastic sampling of the RNA structural alignment space". Nucleic Acids Research. 37 (12): 4063–4075. doi:10.1093/nar/gkp276. PMC 2709569. PMID 19429694.
  17. ^ Hamada, M; Kiryu, H; Mituyama, T; Asai, K (2009). "Prediction of RNA secondary structure using generalized centroid estimators". Bioinformatics. 25 (4): 465–473. doi:10.1093/bioinformatics/btn601. PMID 19095700.
  18. ^ Carvalho, L. E.; Lawrence, C. E. (2008). "Centroid estimation in discrete high- dimensional spaces with applications in biology". Proc Natl Acad Sci. 105 (9): 3209–14. Bibcode:2008PNAS..105.3209C. doi:10.1073/pnas.0712329105. PMC 2265131. PMID 18305160.
  19. ^ Newberg, L. A.; Thompson, W. A.; Colan, S; Smith, T. M.; McCue, L. A.; Lawrence, C. E. (2007). "Centroid estimation in discrete high- dimensional spaces with applications in biology". Bioinformatics. 23 (14): 1718–27. doi:10.1093/bioinformatics/btm241. PMC 2268014. PMID 17488758.
  20. ^ Bellaousov, S; Reuter, Js; Seetin, MG; Mathews, DH (2013). "RNAstructure: Web servers for RNA secondary structure prediction and analysis". Nucleic Acids Research. 41 ((Web Server Issue)): W471-4. doi:10.1093/nar/gkt290. PMC 3692136. PMID 23620284.
  21. ^ Gruber, AR; Lorenz, R; Bernhart, SH; Neuböck, R; Hofacker, IL (2008). "The Vienna RNA websuite". Nucleic Acids Research. 36 (Web Server Issue): W70-4. doi:10.1093/nar/gkn188. PMC 2447809. PMID 18424795.
  22. ^ Mathews, DH; Sabina, J; Turner, DH (1999). "Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure". J. Mol. Biol. 288 (5): 911–40. doi:10.1006/jmbi.1999.2700. PMID 10329189.
  23. ^ Ding, Y.; Lawrence, C. E. (2003). "A statistical sampling algorithm for RNA secondary structure prediction". Nucleic Acids Research. 31 (24): 7280–7301. doi:10.1093/nar/gkg938. PMC 297010. PMID 14654704.
  24. ^ "TOOLS: Nucleic Acid Origami". Science. 300 (5621): 873. 2003. doi:10.1126/science.300.5621.873d. S2CID 220109027.
  25. ^ "Research highlights". Nature. 446 (7136): 586–587. 2007. Bibcode:2007Natur.446..586.. doi:10.1038/446586a. ISSN 0028-0836.
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