Format

Send to

Choose Destination
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W475-9. doi: 10.1093/nar/gkt291. Epub 2013 Apr 29.

The RNAsnp web server: predicting SNP effects on local RNA secondary structure.

Author information

1
Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.

Abstract

The function of many non-coding RNA genes and cis-regulatory elements of messenger RNA largely depends on the structure, which is in turn determined by their sequence. Single nucleotide polymorphisms (SNPs) and other mutations may disrupt the RNA structure, interfere with the molecular function and hence cause a phenotypic effect. RNAsnp is an efficient method to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. The SNP effects are quantified in terms of empirical P-values, which, for computational efficiency, are derived from extensive pre-computed tables of distributions of substitution effects as a function of gene length and GC content. Here, we present a web service that not only provides an interface for RNAsnp but also features a graphical output representation. In addition, the web server is connected to a local mirror of the UCSC genome browser database that enables the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. The RNAsnp web server is freely available at: http://rth.dk/resources/rnasnp/.

PMID:
23630321
PMCID:
PMC3977658
DOI:
10.1093/nar/gkt291
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center