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Sfold information


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]

  1. ^ 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. ^ 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. ^ 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.

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Sfold

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Sfold is a software program developed to predict probable RNA secondary structures through structure ensemble sampling and centroid predictions with a...

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PMC 297010. PMID 14654704. Ding Y, Chan CY, Lawrence CE (July 2004). "Sfold web server for statistical folding and rational design of nucleic acids"...

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C9orf135

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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...

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TEX55

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timetree.org. Retrieved 2019-05-06. "Sfold - Software for Statistical Folding and Studies of Regulatory RNAs". sfold.wadsworth.org. Retrieved 2019-05-06...

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DEPDC1B

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prediction using the other methods. Mfold http://mfold.rna.albany.edu/ Sfold http://sfold.wadsworth.org/ TragetScan http://www.targetscan.org/ Q8WUY9 (DEP1B_HUMAN)...

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C14orf119

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nlm.nih.gov. Retrieved May 3, 2020. "Sfold - Software for Statistical Folding and Studies of Regulatory RNAs". sfold.wadsworth.org. Retrieved May 2, 2020...

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Nucleic acid structure prediction

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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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