{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T14:35:45Z","timestamp":1759847745216},"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>Motivation: Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near-optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for finding effectively the most biologically meaningful alignment in the potentially large set of options.<\/jats:p>\n               <jats:p>Results: We have developed Web-based software that displays near optimal or alternative alignments of two protein or DNA sequences as a continuous moving picture. A WWW interface to a C++ program generates near optimal alignments, which are sent to a Java Applet, which displays them in a series of alignment frames. The Applet aligns residues so that consistently aligned regions remain at a fixed position on the display, while variable regions move. The display can be stopped to examine alignment details.<\/jats:p>\n               <jats:p>Availability: Available at http:\/\/fasta.bioch.virginia.edu\/noptalign. For source code contact the authors at wrp@virginia.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth013","type":"journal-article","created":{"date-parts":[[2004,3,2]],"date-time":"2004-03-02T21:41:06Z","timestamp":1078263666000},"page":"953-958","source":"Crossref","is-referenced-by-count":7,"title":["Visualization of near-optimal sequence alignments"],"prefix":"10.1093","volume":"20","author":[{"given":"Michael E.","family":"Smoot","sequence":"first","affiliation":[]},{"given":"Stephanie A.","family":"Guerlain","sequence":"additional","affiliation":[]},{"given":"William R.","family":"Pearson","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,1,29]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/6\/953\/48905355\/bioinformatics_20_6_953.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/6\/953\/48905355\/bioinformatics_20_6_953.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T18:01:43Z","timestamp":1674669703000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/6\/953\/233513"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,1,29]]},"references-count":0,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2004,4,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth013","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":[[2004,1,29]]}}}