{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T21:46:42Z","timestamp":1761947202387},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2004,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The Server for Quick Alignment Reliability Evaluation (SQUARE) is a Web-based version of the method we developed to predict regions of reliably aligned residues in sequence alignments. Given an alignment between a query sequence and a sequence of known structure, SQUARE is able to predict which residues are reliably aligned. The server accesses a database of profiles of sequences of known three-dimensional structures in order to calculate the scores for each residue in the alignment. SQUARE produces a graphical output of the residue profile-derived alignment scores along with an indication of the reliability of the alignment. In addition, the scores can be compared against template secondary structure, conserved residues and important sites.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.pdg.cnb.uam.es\/servers\/square<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth032","type":"journal-article","created":{"date-parts":[[2004,3,2]],"date-time":"2004-03-02T21:41:06Z","timestamp":1078263666000},"page":"974-975","source":"Crossref","is-referenced-by-count":17,"title":["SQUARE\u2014determining reliable regions in sequence alignments"],"prefix":"10.1093","volume":"20","author":[{"given":"Michael L.","family":"Tress","sequence":"first","affiliation":[{"name":"CNB-CSIC, Calle Darwin, Cantoblanco, 28049 Madrid, Spain"}]},{"given":"Osvaldo","family":"Gra\u00f1a","sequence":"additional","affiliation":[{"name":"CNB-CSIC, Calle Darwin, Cantoblanco, 28049 Madrid, Spain"}]},{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[{"name":"CNB-CSIC, Calle Darwin, Cantoblanco, 28049 Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2004,2,5]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/6\/974\/48905269\/bioinformatics_20_6_974.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/6\/974\/48905269\/bioinformatics_20_6_974.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T17:58:51Z","timestamp":1674669531000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/6\/974\/233556"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,2,5]]},"references-count":0,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2004,4,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth032","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2004,4,12]]},"published":{"date-parts":[[2004,2,5]]}}}