CATANA: a tool for generating comprehensive annotations of alternative transcript events.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
15 04 2019
15 04 2019
Historique:
received:
16
05
2018
revised:
15
08
2018
accepted:
06
09
2018
pubmed:
12
9
2018
medline:
19
2
2020
entrez:
12
9
2018
Statut:
ppublish
Résumé
In higher eukaryotes, the generation of transcript isoforms from a single gene through alternative splicing (AS) and alternative transcription (AT) mechanisms increases functional and regulatory diversities. Annotating these alternative transcript events is essential for genomic studies. However, there are no existing tools that generate comprehensive annotations of all these alternative transcript events including both AS and AT events. In the present study, we develop CATANA, with the encoded exon usage patterns based on the flattened gene model, to identify ten types of AS and AT events. We demonstrate the power and versatility of CATANA by showing greater depth of annotations of alternative transcript events according to either genome annotation or RNA-seq data. CATANA is available on https://github.com/shiauck/CATANA. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 30202999
pii: 5092932
doi: 10.1093/bioinformatics/bty795
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1414-1415Informations de copyright
© The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.