Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Methodology article

Improving pan-genome annotation using whole genome multiple alignment

Samuel V Angiuoli12*, Julie C Dunning Hotopp2, Steven L Salzberg1 and Hervé Tettelin2

Author Affiliations

1 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA

2 Institute for Genome Sciences (IGS), University of Maryland Baltimore, Baltimore, Maryland 21201, USA

For all author emails, please log on.

BMC Bioinformatics 2011, 12:272  doi:10.1186/1471-2105-12-272

Published: 30 June 2011

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.