Show simple item record

dc.contributor.authorYu, G. X.
dc.contributor.authorSnyder, E. E.
dc.contributor.authorBoyle, S. M.
dc.contributor.authorCrasta, O. R.
dc.contributor.authorCzar, M.
dc.contributor.authorMane, S. P.
dc.contributor.authorPurkayastha, A.
dc.contributor.authorSobral, B.
dc.contributor.authorSetubal, J. C.
dc.date.accessioned2019-04-19T18:32:02Z
dc.date.available2019-04-19T18:32:02Z
dc.date.issued2007-06
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/10919/89061
dc.description.abstractWe present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence variants such as genes with disrupted reading frames (split genes) and those with insertions and deletions (indels). For a given genome to be analyzed, GenVar relies on a database containing closely related genomes (such as other species or strains) as well as a few additional reference genomes. GenVar also helps identify gene disruptions probably caused by sequencing errors. We exemplify GenVar's capabilities by presenting results from the analysis of four Brucella genomes. Brucella is an important human pathogen and zoonotic agent. The analysis revealed hundreds of missed gene calls, new split genes and indels, several of which are species specific and hence provide valuable clues to the understanding of the genome basis of Brucella pathogenicity and host specificity.en_US
dc.description.sponsorshipPHS HHS [HHSN266200400035C]
dc.format.mimetypeapplication/pdf
dc.language.isoen_US
dc.rightsCreative Commons Attribution-NonCommercial 2.-3
dc.rights.urihttps://creativecommons.org/licenses/by-nc/2.0/
dc.subjecturease-negative mutant
dc.subjecthelicobacter-pylori
dc.subjectiv secretion
dc.subjectsuis
dc.subjectmelitensis
dc.subjectsequence
dc.subjectabortus
dc.subjectprotein
dc.subjectpurification
dc.subjectcolonize
dc.titleA versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use caseen_US
dc.typeArticle - Refereed
dc.title.serialNucleic Acids Research
dc.identifier.doihttps://doi.org/10.1093/nar/gkm377
dc.identifier.volume35
dc.identifier.issue12
dc.type.dcmitypeText
dc.identifier.pmid17553834
dc.identifier.eissn1362-4962


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record

Creative Commons Attribution-NonCommercial 2.-3
License: Creative Commons Attribution-NonCommercial 2.-3