CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation

Virag Sharma, Peter Schwede, Michael Hiller

Research output: Contribution to journalArticlepeer-review

Abstract

Motivation: Homology-based gene prediction is a powerful concept to annotate newly sequenced genomes. We have previously demonstrated that whole genome alignments can be utilized for accurate comparative coding gene annotation. Results: Here we present CESAR 2.0 that utilizes genome alignments to transfer coding gene annotations from one reference to many other aligned genomes. We show that CESAR 2.0 is 77 times faster and requires 31 times less memory compared to its predecessor. CESAR 2.0 substantially improves the ability to align splice sites that have shifted over larger distances, allowing for precise identification of the exon boundaries in the aligned genome. Finally, CESAR 2.0 supports entire genes, which enables the annotation of joined exons that arose by complete intron deletions. CESAR 2.0 can readily be applied to new genome alignments to annotate coding genes in many other genomes at improved accuracy and without necessitating large-computational resources.

Original languageEnglish
Pages (from-to)3985-3987
Number of pages3
JournalBioinformatics
Volume33
Issue number24
DOIs
Publication statusPublished - 15 Dec 2017
Externally publishedYes

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