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The designation of a confident prediction framework by integrating different predictors followed by consensus prediction, results integration and manual confirmation will improve the prediction of the outer membrane proteome.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In the present study, we used 10 different predictors classified into three groups (subcellular localization, transmembrane \u03b2-barrel protein and lipoprotein predictors) to identify putative OMPs from two available <jats:italic>P. multocida<\/jats:italic> genomes: those of avian strain Pm70 and porcine non-toxigenic strain 3480. Predicted proteins in each group were filtered by optimized criteria for consensus prediction: at least two positive predictions for the subcellular localization predictors, three for the transmembrane \u03b2-barrel protein predictors and one for the lipoprotein predictors. The consensus predicted proteins were integrated from each group into a single list of proteins. We further incorporated a manual confirmation step including a public database search against PubMed and sequence analyses, e.g. sequence and structural homology, conserved motifs\/domains, functional prediction, and protein-protein interactions to enhance the confidence of prediction. As a result, we were able to confidently predict 98 putative OMPs from the avian strain genome and 107 OMPs from the porcine strain genome with 83% overlap between the two genomes.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The bioinformatic framework developed in this study has increased the number of putative OMPs identified in <jats:italic>P. multocida<\/jats:italic> and allowed these OMPs to be identified with a higher degree of confidence. Our approach can be applied to investigate the outer membrane proteomes of other Gram-negative bacteria.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-63","type":"journal-article","created":{"date-parts":[[2012,4,28]],"date-time":"2012-04-28T00:14:48Z","timestamp":1335572088000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation"],"prefix":"10.1186","volume":"13","author":[{"given":"Teerasak","family":"E-komon","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Burchmore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pawel","family":"Herzyk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Davies","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2012,4,27]]},"reference":[{"key":"5244_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1574-6968.2006.00442.x","volume":"265","author":"M Harper","year":"2006","unstructured":"Harper M, Boyce JD, Adler B: Pasteurella multocid pathogenesis: 125 years after Pasteur. 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