Improved transcript isoform discovery using ORF graphs.

ABSTRACT:

Motivation

High-throughput sequencing of RNA in vivo facilitates many applications, not the least of which is the cataloging of variant splice isoforms of protein-coding messenger RNAs. Although many solutions have been proposed for reconstructing putative isoforms from deep sequencing data, these generally take as their substrate the collective alignment structure of RNA-seq reads and ignore the biological signals present in the actual nucleotide sequence. The majority of these solutions are graph-theoretic, relying on a splice graph representing the splicing patterns and exon expression levels indicated by the spliced-alignment process.

Results

We show how to augment splice graphs with additional information reflecting the biology of transcription, splicing and translation

SUBMITTER: Majoros WH 

PROVIDER: S-EPMC4288128 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature