Improved transcript isoform discovery using ORF graphs.
Bioinformatics
; 30(14): 1958-64, 2014 Jul 15.
Article
em En
| MEDLINE
| ID: mdl-24659106
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, 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/.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Fases de Leitura Aberta
/
Análise de Sequência de RNA
/
Sequenciamento de Nucleotídeos em Larga Escala
/
Isoformas de RNA
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2014
Tipo de documento:
Article