{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T22:03:18Z","timestamp":1717711398990},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"suppl_1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2003,7,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Evolutionary comparison leads to efficient functional characterisation of hypothetical proteins. Here, our goal is to map specific sequence patterns to putative functional classes. The evolutionary signal stands out most clearly in a maximally diverse set of homologues. This diversity, however, leads to a number of technical difficulties. The targeted patterns\u2014as gleaned from structure comparisons\u2014are too sparse for statistically significant signals of sequence similarity and accurate multiple sequence alignment.<\/jats:p>\n               <jats:p>Results: We address this problem by a fuzzy alignment model, which probabilistically assigns residues to structurally equivalent positions (attributes) of the proteins. We then apply multivariate analysis to the \u2018attributes x proteins\u2019 matrix. The dimensionality of the space is reduced using non-negative matrix factorization. The method is general, fully automatic and works without assumptions about pattern density, minimum support, explicit multiple alignments, phylogenetic trees, etc. We demonstrate the discovery of biologically meaningful patterns in an extremely diverse superfamily related to urease.<\/jats:p>\n               <jats:p>Contact: Liisa.Holm@Helsinki.fi<\/jats:p>\n               <jats:p>*To whom correspondence should be addressed.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btg1017","type":"journal-article","created":{"date-parts":[[2003,7,10]],"date-time":"2003-07-10T23:49:03Z","timestamp":1057880943000},"page":"i130-i137","source":"Crossref","is-referenced-by-count":38,"title":["Sensitive pattern discovery with \u2018fuzzy\u2019 alignments of distantly\nrelated proteins"],"prefix":"10.1093","volume":"19","author":[{"given":"Andreas","family":"Heger","sequence":"first","affiliation":[{"name":"Institute of Biotechnology, P.O. Box 56, 00014 University of Helsinki Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liisa","family":"Holm","sequence":"additional","affiliation":[{"name":"Institute of Biotechnology, P.O. Box 56, 00014 University of Helsinki Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2003,7,3]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_1\/i130\/227841","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_1\/i130\/227841","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T18:44:32Z","timestamp":1674672272000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_1\/i130\/227841"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,7,3]]},"references-count":0,"journal-issue":{"issue":"suppl_1","published-print":{"date-parts":[[2003,7,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btg1017","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2003,7,3]]},"published":{"date-parts":[[2003,7,3]]}}}