{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T21:35:48Z","timestamp":1782596148501,"version":"3.54.5"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3166,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: An estimated 25% of all eukaryotic proteins contain repeats, which underlines the importance of duplication for evolving new protein functions. Internal repeats often correspond to structural or functional units in proteins. Methods capable of identifying diverged repeated segments or domains at the sequence level can therefore assist in predicting domain structures, inferring hypotheses about function and mechanism, and investigating the evolution of proteins from smaller fragments.<\/jats:p>\n               <jats:p>Results: We present HHrepID, a method for the de novo identification of repeats in protein sequences. It is able to detect the sequence signature of structural repeats in many proteins that have not yet been known to possess internal sequence symmetry, such as outer membrane \u03b2-barrels. HHrepID uses HMM\u2013HMM comparison to exploit evolutionary information in the form of multiple sequence alignments of homologs. In contrast to a previous method, the new method (1) generates a multiple alignment of repeats; (2) utilizes the transitive nature of homology through a novel merging procedure with fully probabilistic treatment of alignments; (3) improves alignment quality through an algorithm that maximizes the expected accuracy; (4) is able to identify different kinds of repeats within complex architectures by a probabilistic domain boundary detection method and (5) improves sensitivity through a new approach to assess statistical significance.<\/jats:p>\n               <jats:p>Availability: Server: http:\/\/toolkit.tuebingen.mpg.de\/hhrepid; Executables: ftp:\/\/ftp.tuebingen.mpg.de\/pub\/protevo\/HHrepID<\/jats:p>\n               <jats:p>Contact: \u00a0soeding@lmb.uni-muenchen.de<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn039","type":"journal-article","created":{"date-parts":[[2008,2,2]],"date-time":"2008-02-02T01:25:55Z","timestamp":1201915555000},"page":"807-814","source":"Crossref","is-referenced-by-count":145,"title":["<i>De novo<\/i> identification of highly diverged protein repeats by probabilistic consistency"],"prefix":"10.1093","volume":"24","author":[{"given":"A.","family":"Biegert","sequence":"first","affiliation":[{"name":"1 Department for Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 T\u00fcbingen and 2Gene Center Munich, University of Munich (LMU), Feodor-Lynen-Str. 25, 81377 Munich, Germany"},{"name":"1 Department for Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 T\u00fcbingen and 2Gene Center Munich, University of Munich (LMU), Feodor-Lynen-Str. 25, 81377 Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J.","family":"S\u00f6ding","sequence":"additional","affiliation":[{"name":"1 Department for Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 T\u00fcbingen and 2Gene Center Munich, University of Munich (LMU), Feodor-Lynen-Str. 25, 81377 Munich, Germany"},{"name":"1 Department for Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 T\u00fcbingen and 2Gene Center Munich, University of Munich (LMU), Feodor-Lynen-Str. 25, 81377 Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2008,2,1]]},"reference":[{"key":"2023020209514077400_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucl. 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