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
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 ]
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 ]