Improving pan-genome annotation using whole genome multiple alignment

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. Conc...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Samuel V. Angiuoli, Julie C. Dunning Hotopp, Steven L. Salzberg, Herve Tettelin
• Keywords: Biometrics, BMCBI 2011, Genome Annotation, Microbial Genomes, Translation Initiation