{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T10:35:04Z","timestamp":1761129304171,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"9","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Not only sequence data continue to outpace annotation information, but also the problem is further exacerbated when organisms are underrepresented in the annotation databases. This is the case with non-human-pathogenic viruses which occur frequently in metagenomic projects. Thus, there is a need for tools capable of detecting and classifying viral sequences.<\/jats:p>\n               <jats:p>Results: We describe VIRALpro a new effective tool for identifying capsid and tail protein sequences, which are the cornerstones toward viral sequence annotation and viral genome classification.<\/jats:p>\n               <jats:p>Availability and implementation: The data, software and corresponding web server are available from http:\/\/scratch.proteomics.ics.uci.edu as part of the SCRATCH suite.<\/jats:p>\n               <jats:p>Contact: \u00a0clovis.galiez@inria.fr or pfbaldi@uci.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv727","type":"journal-article","created":{"date-parts":[[2016,2,14]],"date-time":"2016-02-14T23:14:19Z","timestamp":1455491659000},"page":"1405-1407","source":"Crossref","is-referenced-by-count":22,"title":["VIRALpro: a tool to identify viral capsid and tail sequences"],"prefix":"10.1093","volume":"32","author":[{"given":"Clovis","family":"Galiez","sequence":"first","affiliation":[{"name":"1 INRIA, Campus De Beaulieu, Rennes Cedex, 35042, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christophe N.","family":"Magnan","sequence":"additional","affiliation":[{"name":"2 Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francois","family":"Coste","sequence":"additional","affiliation":[{"name":"1 INRIA, Campus De Beaulieu, Rennes Cedex, 35042, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Baldi","sequence":"additional","affiliation":[{"name":"2 Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,1,5]]},"reference":[{"key":"2023020112224632200_btv727-B1","doi-asserted-by":"crossref","first-page":"27:1","DOI":"10.1145\/1961189.1961199","article-title":"Libsvm: a library for support vector machines","volume":"2","author":"Chang","year":"2011","journal-title":". ACM Trans. Intell. Syst. Technol"},{"key":"2023020112224632200_btv727-B2","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1126\/science.1127404","article-title":"Metagenomic analysis of coastal RNA virus communities","volume":"312","author":"Culley","year":"2006","journal-title":"Science"},{"key":"2023020112224632200_btv727-B3","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1142\/9781848165632_0019","volume-title":"Proceedings of the 20th International Conference on Genome Informatics 2009","author":"Eddy","year":"2009"},{"key":"2023020112224632200_btv727-B4","first-page":"933","article-title":"An efficient boosting algorithm for combining preferences","volume":"4","author":"Freund","year":"2003","journal-title":"J. Mach. Learn. Res"},{"volume-title":"ISMB\/ECCB 2015 Satellite Meeting\u20143DSIG: Structural Bioinformatics and Computational Biophysics","year":"2015","author":"Galiez","key":"2023020112224632200_btv727-B5"},{"key":"2023020112224632200_btv727-B6","doi-asserted-by":"crossref","first-page":"12798","DOI":"10.1073\/pnas.1305956110","article-title":"Twelve previously unknown phage genera are ubiquitous in global oceans","volume":"110","author":"Holmfeldt","year":"2013","journal-title":"Proc. Natl Acad. Sci"},{"key":"2023020112224632200_btv727-B7","doi-asserted-by":"crossref","first-page":"e57355","DOI":"10.1371\/journal.pone.0057355","article-title":"The pacific ocean virome (pov): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology","volume":"8","author":"Hurwitz","year":"2013","journal-title":"PLoS One"},{"key":"2023020112224632200_btv727-B8","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1016\/j.cub.2014.07.046","article-title":"Decoupling physical from biological processes to assess the impact of viruses on a mesoscale algal bloom","volume":"24","author":"Lehahn","year":"2014","journal-title":"Curr. Biol"},{"key":"2023020112224632200_btv727-B9","doi-asserted-by":"crossref","first-page":"2592","DOI":"10.1093\/bioinformatics\/btu352","article-title":"SSpro\/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity","volume":"30","author":"Magnan","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020112224632200_btv727-B10","doi-asserted-by":"crossref","first-page":"bar009","DOI":"10.1093\/database\/bar009","article-title":"Uniprot knowledgebase: a hub of integrated protein data","volume":"2011","author":"Magrane","year":"2011","journal-title":"Database"},{"key":"2023020112224632200_btv727-B11","doi-asserted-by":"crossref","first-page":"e1002657","DOI":"10.1371\/journal.pcbi.1002657","article-title":"Artificial neural networks trained to detect viral and phage structural proteins","volume":"8","author":"Seguritan","year":"2012","journal-title":"PLoS Comput. Biol"},{"key":"2023020112224632200_btv727-B12","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1038\/nrmicro1750","article-title":"Marine viruses major players in the global ecosystem","volume":"5","author":"Suttle","year":"2007","journal-title":"Nat. Rev. Microbiol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/9\/1405\/49019438\/bioinformatics_32_9_1405.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/9\/1405\/49019438\/bioinformatics_32_9_1405.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:28:25Z","timestamp":1675290505000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/9\/1405\/1743663"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,1,5]]},"references-count":12,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2016,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv727","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2016,5,1]]},"published":{"date-parts":[[2016,1,5]]}}}