Improving pan-genome annotation using whole genome multiple alignment
| dc.contributor.author | Angiuoli, Samuel V | |
| dc.contributor.author | Dunning Hotopp, Julie C | |
| dc.contributor.author | Salzberg, Steven L | |
| dc.contributor.author | Tettelin, Herve | |
| dc.date.accessioned | 2013-01-10T20:42:51Z | |
| dc.date.available | 2013-01-10T20:42:51Z | |
| dc.date.issued | 2011-06-30 | |
| dc.description.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. | en_US |
| dc.description.uri | https://doi.org/10.1186/1471-2105-12-272 | |
| dc.identifier.citation | Angiuoli, S.V., Dunning Hotopp, J.C., Salzberg, S.L. et al. Improving pan-genome annotation using whole genome multiple alignment. BMC Bioinformatics 12, 272 (2011). | en_US |
| dc.identifier.uri | http://hdl.handle.net/1903/13352 | |
| dc.language.iso | en_US | en_US |
| dc.relation.isAvailableAt | Cell Biology & Molecular Genetics | en_us |
| dc.relation.isAvailableAt | Digital Repository at the University of Maryland | en_us |
| dc.relation.isAvailableAt | College of Computer, Mathematical & Natural Sciences | en_us |
| dc.relation.isAvailableAt | University of Maryland (College Park, MD) | en_us |
| dc.subject | pan-genomes | en_US |
| dc.subject | Genome annotations | en_US |
| dc.subject | Mugsy-Annotator | en_US |
| dc.title | Improving pan-genome annotation using whole genome multiple alignment | en_US |
| dc.type | Article | en_US |