title: Improving pan-genome annotation using whole genome multiple alignment.
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.
authors: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. angiuoli@umiacs.umd.edu
authors: Samuel V
authors: SV
authors: Angiuoli
authors: Julie C
authors: JC
authors: Dunning Hotopp
authors: Steven L
authors: SL
authors: Salzberg
authors: Hervé
authors: H
authors: Tettelin
mesh_terms: D001419:Bacteria / Q000235:genetics*; D002874:Chromosome Mapping; D016680:Genome, Bacterial; D058977:Molecular Sequence Annotation; D016415:Sequence Alignment / Q000379:methods*