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Improving pan-genome annotation using whole genome multiple alignment

Authors
  • Angiuoli, Samuel V1, 2
  • Dunning Hotopp, Julie C2
  • Salzberg, Steven L1
  • Tettelin, Hervé2
  • 1 University of Maryland, Center for Bioinformatics and Computational Biology, College Park, MD, 20742, USA , College Park (United States)
  • 2 University of Maryland Baltimore, Institute for Genome Sciences (IGS), Baltimore, Maryland, 21201, USA , Baltimore (United States)
Type
Published Article
Journal
BMC Bioinformatics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Jun 30, 2011
Volume
12
Issue
1
Identifiers
DOI: 10.1186/1471-2105-12-272
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundRapid 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.ResultsWe 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.ConclusionsWhole 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.

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