{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T15:53:41Z","timestamp":1761580421599},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Biologists frequently align multiple biological sequences to determine consensus sequences and\/or search for predominant residues and conserved regions. Particularly, determining conserved regions in an alignment is one of the most important activities. Since protein sequences are often several-hundred residues or longer, it is difficult to distinguish biologically important conserved regions (motifs or domains) from others. The widely used tools, Logos, Al2co, Confind, and the entropy-based method, often fail to highlight such regions. Thus a computational tool that can highlight biologically important regions accurately will be highly desired.<\/jats:p>\n               <jats:p>Results: This paper presents a new scoring scheme ARCS (Aggregated Related Column Score) for aligned biological sequences. ARCS method considers not only the traditional character similarity measure but also column correlation. In an extensive experimental evaluation using 533 PROSITE patterns, ARCS is able to highlight the motif regions with up to 77.7% accuracy corresponding to the top three peaks.<\/jats:p>\n               <jats:p>Availability: The source code is available on and<\/jats:p>\n               <jats:p>Contacts: jiong.yang@case.edu, sunkim2@indiana.edu<\/jats:p>\n               <jats:p>Supplementary Material: \u00a0 and<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl398","type":"journal-article","created":{"date-parts":[[2006,7,27]],"date-time":"2006-07-27T00:58:50Z","timestamp":1153961930000},"page":"2326-2332","source":"Crossref","is-referenced-by-count":9,"title":["ARCS: an aggregated related column scoring scheme for aligned sequences"],"prefix":"10.1093","volume":"22","author":[{"given":"Bin","family":"Song","sequence":"first","affiliation":[{"name":"Electrical Engineering and Computer Science Department, Case Western Reserve University 1 \u00a0 1 \u00a0 \u00a0 Cleveland, OH, USA"}]},{"given":"Jeong-Hyeon","family":"Choi","sequence":"additional","affiliation":[{"name":"School of Informatics, Indiana University 2 \u00a0 2 \u00a0 \u00a0 Bloomington, IN, USA"}]},{"given":"Guangyu","family":"Chen","sequence":"additional","affiliation":[{"name":"Electrical Engineering and Computer Science Department, Case Western Reserve University 1 \u00a0 1 \u00a0 \u00a0 Cleveland, OH, USA"}]},{"given":"Jacek","family":"Szymanski","sequence":"additional","affiliation":[{"name":"Electrical Engineering and Computer Science Department, Case Western Reserve University 1 \u00a0 1 \u00a0 \u00a0 Cleveland, OH, USA"}]},{"given":"Guo-Qiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Electrical Engineering and Computer Science Department, Case Western Reserve University 1 \u00a0 1 \u00a0 \u00a0 Cleveland, OH, USA"}]},{"given":"Anthony K. 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