SAW: a method to identify splicing events from RNA-Seq data based on splicing fingerprints.

ABSTRACT: Splicing event identification is one of the most important issues in the comprehensive analysis of transcription profile. Recent development of next-generation sequencing technology has generated an extensive profile of alternative splicing. However, while many of these splicing events are between exons that are relatively close on genome sequences, reads generated by RNA-Seq are not limited to alternative splicing between close exons but occur in virtually all splicing events. In this work, a novel method, SAW, was proposed for the identification of all splicing events based on short reads from RNA-Seq. It was observed that short reads not in known gene models are actually absent words from known gene sequences. An efficient method to filter and cluster these short reads by fingerprint fr

SUBMITTER: Ning K 

PROVIDER: S-EPMC2919401 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature