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. 2004 Jul 1;32(Web Server issue):W135-41.
doi: 10.1093/nar/gkh449.

Sfold web server for statistical folding and rational design of nucleic acids

Ye Ding  1 , Chi Yu Chan, Charles E Lawrence
Affiliations

Sfold web server for statistical folding and rational design of nucleic acids

Ye Ding et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Figure 1
Figure 1
Regional profile (window width W = 4) for the region between nt 201 and 400 of the rabbit β-globin mRNA (GenBank accession no. V00879). Sites with high probabilities are predicted to be accessible.
Figure 2
Figure 2
Internal stability profile (15) for the siRNA targeting positions 44–64 of the rabbit β-globin mRNA.
Figure 3
Figure 3
Probability profile (window width W = 1 for ribozyme applications) for the region of the cleavage triplet G87UC89 and its two flanking sequences of 15 each for the rabbit β-globin mRNA.
Figure 4
Figure 4
Two-dimensional histograms (2Dhist) for a sample of 1000 structures generated for Leptomonas collosoma spliced leader RNA of 56 nt in length (23). As an example of the option of ‘with base pair probabilities’, the sampling estimate of the probability for the base pair between nt 25 and 29 is shown to be 0.681 when the mouse is pointed at the solid square positioned at (25,29).
Figure 5
Figure 5
Secondary structure diagram generated by a modified version of the naview program (24) for a predicted structure of Leptomonas collosoma spliced leader RNA.
See this image and copyright information in PMC

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