Sequence analysis Advance Access publication March 22, 2014 Improved transcript isoform discovery using ORF graphs

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 ma-jority of these solutions are graph-theoretic, relying on a splice graph representing the splicing patterns and exon expression levels indi-cated by the spliced-alignment process. Results: We show how to augment splice graphs with additional in-formation reflecting the biology of transcription, splicing and transla-tion, to produce what we call an ORF (open reading frame) graph. We then show how ORF graphs can be used to produce isoform predic-tions with higher accuracy than current state-of-the-art approaches. Availability and implementation: RSVP is available as Cþþ source code under an open-source licence