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RNAsnp

Efficient detection of local RNA secondary structure changes induced by SNPs

Introduction

Structural characteristics are essential for the functioning of many non-coding RNAs and cis-regulatory elements of mRNAs. Single Nucleotide Polymorphisms (SNPs) may disrupt these structures, interfere with their molecular function, and hence cause a phenotypic effect. RNA folding algorithms can provide detailed insights into structural effects of SNPs. The global measures employed so far suffer from limited accuracy of folding programs on large RNAs and are computationally too demanding for genome-wide applications. Thus we developed RNAsnp [1] which focuses on the local regions of maximal structural change between wild-type and mutant. The mutation effects are quantified in terms of empirical p-values. To this end, the RNAsnp software uses extensive precomputed tables of the distribution of SNP effects as function of sequence length, GC content and SNP position.

The web server [2] based on RNAsnp provides a convenient interface to provide input data to RNAsnp and to select different modes of operation. It helps visualize the output using informative graphical representation, such as dot plot matrices comparing pair probabilities for wild-type and mutant. 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 of interest for analysis and to visualize the results in the UCSC genome browser



  1. Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J. RNAsnp: Efficient detection of local RNA secondary structure changes induced by SNPs. Human Mutation 34:546-556, 2013 [ PubMed ]

  2. Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J. The RNAsnp Web Server: Predicting SNP effects on local RNA secondary structure Nucleic Acid Res. 41(W1):W475-W479, 2013 [ PubMed ]

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