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 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, to produce what we call an ORF (open reading frame) graph. We then show how ORF graphs can be used to produce isoform predictions with higher accuracy than current state-of-the-art approaches. AVAILABILITY AND IMPLEMENTATION: RSVP is available as C++ source code under an open-source licence: http://ohlerlab.mdc-berlin.de/software/RSVP/.
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Related Subject Headings
- Software
- Sequence Analysis, RNA
- RNA Splicing
- RNA Isoforms
- Open Reading Frames
- Humans
- High-Throughput Nucleotide Sequencing
- Exons
- Bioinformatics
- Arabidopsis
Citation
Published In
DOI
EISSN
Publication Date
Volume
Issue
Start / End Page
Location
Related Subject Headings
- Software
- Sequence Analysis, RNA
- RNA Splicing
- RNA Isoforms
- Open Reading Frames
- Humans
- High-Throughput Nucleotide Sequencing
- Exons
- Bioinformatics
- Arabidopsis