A note about computing all local alignments.
A recent paper in this journal by G. Barton proposed an efficient algorithm for locating locally optimal alignments between two sequences. Although the paper claims that all such alignments are found, the approach frequently fails to detect some of the significant matches. This note explains the deficiency.
Miller
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W
Department of Computer Science and Engineering, Pennsylvania State University, University Park 16802.
Boguski
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M
D000465:Algorithms; D019883:Alkyl and Aryl Transferases; D000818:Animals; D001921:Brain / Q000201:enzymology; D004247:DNA / Q000235:genetics; D051231:Farnesyltranstransferase; D005656:Fungal Proteins / Q000235:genetics; D011506:Proteins / Q000235:genetics; D051381:Rats; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D014166:Transferases / Q000235:genetics
D005656:Fungal Proteins; D011506:Proteins; C077378:RAM2 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D004247:DNA; D014166:Transferases; D019883:Alkyl and Aryl Transferases; D051231:Farnesyltranstransferase