Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites.

ABSTRACT:

Background

Some single nucleotide polymorphisms (SNPs) are known to modify the risk of developing certain diseases or the reaction to drugs. Due to next generation sequencing methods the number of known human SNPs has grown. Not all SNPs lead to a modified protein, which may be the origin of a disease. Therefore, the recognition of functional SNPs is needed. Because most SNP annotation tools look for SNPs which lead to an amino acid exchange or a premature stop, we designed a new tool called AASsites which searches for SNPs which modify splicing.

Results

AASsites uses several gene prediction programs and open reading frame prediction to compare the wild type (wt) and the variant gene sequence. The results of the comparison are combined by a handmade rule system to classify a

SUBMITTER: Faber K 

PROVIDER: S-EPMC3194194 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature