Sfold web server for statistical folding and rational design of nucleic acids. The Sfold web server provides user-friendly access to Sfold, a recently developed nucleic acid folding software package, via the World Wide Web (WWW). The software is based on a new statistical sampling paradigm for the prediction of RNA secondary structure. One of the main objectives of this software is to offer computational tools for the rational design of RNA-targeting nucleic acids, which include small interfering RNAs (siRNAs), antisense oligonucleotides and trans-cleaving ribozymes for gene knock-down studies. The methodology for siRNA design is based on a combination of RNA target accessibility prediction, siRNA duplex thermodynamic properties and empirical design rules. Our approach to target accessibility evaluation is an original extension of the underlying RNA folding algorithm to account for the likely existence of a population of structures for the target mRNA. In addition to the application modules Sirna, Soligo and Sribo for siRNAs, antisense oligos and ribozymes, respectively, the module Srna offers comprehensive features for statistical representation of sampled structures. Detailed output in both graphical and text formats is available for all modules. The Sfold server is available at http://sfold.wadsworth.org and http://www.bioinfo.rpi.edu/applications/sfold.

References in zbMATH (referenced in 13 articles , 1 standard article )

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  1. Bundschuh, Ralf: Unified approach to partition functions of RNA secondary structures (2014)
  2. Condon, Anne; Jabbari, Hosna: Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges (2009)
  3. Bompfünewerer, Athanasius F.; Backofen, Rolf; Bernhart, Stephan H.; Hertel, Jana; Hofacker, Ivo L.; Stadler, Peter F.; Will, Sebastian: Variations on RNA folding and alignment: Lessons from Benasque (2008)
  4. Chan, Chi Yu; Ding, Ye: Boltzmann ensemble features of RNA secondary structures: a comparative analysis of biological RNA sequences and random shuffles (2008)
  5. Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell: Computational methods in noncoding RNA research (2008)
  6. Metzler, Dirk; Nebel, Markus E.: Predicting RNA secondary structures with pseudoknots by MCMC sampling (2008)
  7. Ponty, Yann: Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy (2008)
  8. Gąsieniec, Leszek; Li, Cindy Y.; Sant, Paul; Wong, Prudence W. H.: Randomized probe selection algorithm for microarray design (2007)
  9. Gharaibeh, Raad Z.; Fodor, Anthony A.; Gibas, Cynthia J.: Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates (2007)
  10. Prohaska, Sonja J.; Mosig, Axel; Stadler, Peter F.: Regulatory signals in genomic sequences (2007)
  11. Jeffries, Clark; Perkins, Diana O.; Jarstfer, Michael: Systematic discovery of the grammar of translational inhibition by RNA hairpins (2006)
  12. Zhang, Baohong; Pan, Xiaoping; Wang, Qinglian; Cobb, George P.; Anderson, Todd A.: Computational identification of microRNAs and their targets (2006)
  13. Ding, Ye; Chan, Chi Yu; Lawrence, Charles E.: Sfold web server for statistical folding and rational design of nucleic acids. (2004) ioport