Sfold

Last updated
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;22 years ago (2003-04-01)
Repository github.com/Ding-RNA-Lab/Sfold
Operating system Linux
Website www.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]

Contents

Development

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 comprehensive review, [9] with both the sampling approach and the centroid predictions being discussed. [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] and 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

Sfold runs under Linux, 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.

References

  1. 1 2 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. 1 2 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. Bibcode:2001Natur.411..494E. 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. 1 2 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. 1 2 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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