RNA secondary structure prediction and application software
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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 release
1 April 2003; 21 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]
^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.
^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.
^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.
^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.
Sfold is a software program developed to predict probable RNA secondary structures through structure ensemble sampling and centroid predictions with a...
PMC 297010. PMID 14654704. Ding Y, Chan CY, Lawrence CE (July 2004). "Sfold web server for statistical folding and rational design of nucleic acids"...
nlm.nih.gov. Retrieved May 3, 2020. "Sfold - Software for Statistical Folding and Studies of Regulatory RNAs". sfold.wadsworth.org. Retrieved May 2, 2020...
gov/nuccore/809279636?report=fasta Archived 2016-09-15 at the Wayback Machine Sfold, Srna, http://sfold.wadsworth.org/cgi-bin/showcentroid.pl Archived 2016-05-06 at the...
prediction using the other methods. Mfold http://mfold.rna.albany.edu/ Sfold http://sfold.wadsworth.org/ TragetScan http://www.targetscan.org/ Q8WUY9 (DEP1B_HUMAN)...
sample structures from the Boltzmann ensemble, as exemplified by the program SFOLD. The program generates a statistical sample of all possible RNA secondary...
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