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BMC Bioinformatics. 2011 Jun 30;12:272. doi: 10.1186/1471-2105-12-272.

Improving pan-genome annotation using whole genome multiple alignment.

Author information

1
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. angiuoli@umiacs.umd.edu

Abstract

BACKGROUND:

Rapid annotation and comparisons of genomes from multiple isolates (pan-genomes) is becoming commonplace due to advances in sequencing technology. Genome annotations can contain inconsistencies and errors that hinder comparative analysis even within a single species. Tools are needed to compare and improve annotation quality across sets of closely related genomes.

RESULTS:

We introduce a new tool, Mugsy-Annotator, that identifies orthologs and evaluates annotation quality in prokaryotic genomes using whole genome multiple alignment. Mugsy-Annotator identifies anomalies in annotated gene structures, including inconsistently located translation initiation sites and disrupted genes due to draft genome sequencing or pseudogenes. An evaluation of species pan-genomes using the tool indicates that such anomalies are common, especially at translation initiation sites. Mugsy-Annotator reports alternate annotations that improve consistency and are candidates for further review.

CONCLUSIONS:

Whole genome multiple alignment can be used to efficiently identify orthologs and annotation problem areas in a bacterial pan-genome. Comparisons of annotated gene structures within a species may show more variation than is actually present in the genome, indicating errors in genome annotation. Our new tool Mugsy-Annotator assists re-annotation efforts by highlighting edits that improve annotation consistency.

PMID:
21718539
PMCID:
PMC3142524
DOI:
10.1186/1471-2105-12-272
[Indexed for MEDLINE]
Free PMC Article
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