{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T10:27:58Z","timestamp":1760783278107},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Detection of distant homology is a widely used computational approach for studying protein evolution, structure and function. Here, we report a homology search web server based on sequence profile\u2013profile comparison. The user may perform searches in one of several regularly updated profile databases using either a single sequence or a multiple sequence alignment as an input. The same profile databases can also be downloaded for local use. The capabilities of the server are illustrated with the identification of new members of the highly diverse PD-(D\/E)XK nuclease superfamily.<\/jats:p><jats:p>Availability: \u00a0http:\/\/www.ibt.lt\/bioinformatics\/coma\/<\/jats:p><jats:p>Contact: \u00a0venclovas@ibt.lt<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq306","type":"journal-article","created":{"date-parts":[[2010,6,8]],"date-time":"2010-06-08T01:20:28Z","timestamp":1275960028000},"page":"1905-1906","source":"Crossref","is-referenced-by-count":27,"title":["COMA server for protein distant homology search"],"prefix":"10.1093","volume":"26","author":[{"given":"Mindaugas","family":"Margelevi\u010dius","sequence":"first","affiliation":[{"name":"Institute of Biotechnology, Grai\u010di\u016bno 8, LT-02241 Vilnius, Lithuania"}]},{"given":"Mindaugas","family":"Laganeckas","sequence":"additional","affiliation":[{"name":"Institute of Biotechnology, Grai\u010di\u016bno 8, LT-02241 Vilnius, Lithuania"}]},{"given":"\u010ceslovas","family":"Venclovas","sequence":"additional","affiliation":[{"name":"Institute of Biotechnology, Grai\u010di\u016bno 8, LT-02241 Vilnius, Lithuania"}]}],"member":"286","published-online":{"date-parts":[[2010,6,6]]},"reference":[{"key":"2023012508002518400_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":"Nucleic Acids Res."},{"key":"2023012508002518400_B2","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1002\/pro.297","article-title":"A galaxy of folds","volume":"19","author":"Alva","year":"2010","journal-title":"Protein Sci."},{"key":"2023012508002518400_B3","doi-asserted-by":"crossref","first-page":"3767","DOI":"10.1074\/jbc.M709617200","article-title":"Pet127 governs a 5\u2032-&gt; 3\u2032-exonuclease important in maturation of apocytochrome b mRNA in Saccharomyces cerevisiae","volume":"283","author":"Fekete","year":"2008","journal-title":"J. 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