{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T01:09:23Z","timestamp":1773277763259,"version":"3.50.1"},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2004,5,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation:In recent years, several methods have been proposed for aligning two protein sequence profiles, with reported improvements in alignment accuracy and homolog discrimination versus sequence\u2013sequence methods (e.g. BLAST) and profile\u2013sequence methods (e.g. PSI-BLAST). Profile\u2013profile alignment is also the iterated step in progressive multiple sequence alignment algorithms such as CLUSTALW. However, little is known about the relative performance of different profile\u2013profile scoring functions. In this work, we evaluate the alignment accuracy of 23 different profile\u2013profile scoring functions by comparing alignments of 488 pairs of sequences with identity \u226430% against structural alignments. We optimize parameters for all scoring functions on the same training set and use profiles of alignments from both PSI-BLAST and SAM-T99. Structural alignments are constructed from a consensus between the FSSP database and CE structural aligner. We compare the results with sequence\u2013sequence and sequence\u2013profile methods, including BLAST and PSI-BLAST.<\/jats:p>\n               <jats:p>Results: We find that profile\u2013profile alignment gives an average improvement over our test set of typically 2\u20133% over profile\u2013sequence alignment and \u223c40% over sequence\u2013sequence alignment. No statistically significant difference is seen in the relative performance of most of the scoring functions tested. Significantly better results are obtained with profiles constructed from SAM-T99 alignments than from PSI-BLAST alignments.<\/jats:p>\n               <jats:p>Availability: Source code, reference alignments and more detailed results are freely available at http:\/\/phylogenomics.berkeley.edu\/profilealignment\/<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth090","type":"journal-article","created":{"date-parts":[[2004,3,2]],"date-time":"2004-03-02T21:41:06Z","timestamp":1078263666000},"page":"1301-1308","source":"Crossref","is-referenced-by-count":90,"title":["A comparison of scoring functions for protein sequence profile alignment"],"prefix":"10.1093","volume":"20","author":[{"given":"Robert C.","family":"Edgar","sequence":"first","affiliation":[]},{"given":"Kimmen","family":"Sj\u00f6lander","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,2,12]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/8\/1301\/48905385\/bioinformatics_20_8_1301.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/8\/1301\/48905385\/bioinformatics_20_8_1301.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T16:54:20Z","timestamp":1674665660000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/8\/1301\/210230"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,2,12]]},"references-count":0,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2004,5,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth090","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2004,5,22]]},"published":{"date-parts":[[2004,2,12]]}}}