<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi all,<DIV> I'm in need of a fast sequence matching algorithm for DNA/RNA/protein sequences. My query searches are relatively short (<100bp) and 'subject' sequence is on the order of 10kb. At the moment, I'm using the span() function in python's regular expression module to return all matches:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>matches = [match.span() for match in re.finditer(re.escape(str(query)), str(subject), re.IGNORECASE )]</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV> This basically returns all coordinates of my query against subject as a list of tuples (match start, match stop), but its somewhat sluggish for my needs. Is there a way to do it faster within python?</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Sagar Damle</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Graduate Student</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Biology Division, Caltech</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">1200 E. California Blvd, 156-29</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Pasadena, CA 91125</FONT></P> </DIV><BR></BODY></HTML>