<p>I have a few hundred yeast sequences (20-80bp long) and I want to find common motifs (conserved bases at certain indices) in them. I am using a Mac</p>

<p>I would recommend <a href='http://meme.sdsc.edu/meme4_3_0/intro.html'>MEME</a> as others, however <a href='http://159.149.109.9/modtools/'>Weeder</a> is also very easy to install and run on a Mac. It is word based and runs a lot faster than Meme, with a far fewer options. </p>

<p>If you would like something to run specifically on your Mac you could try <a href='http://wiki.github.com/mz2/imotifs/'>iMotifs</a>, which incorporates the <a href='http://www.sanger.ac.uk/resources/software/nestedmica/'>NestedMICA</a> algorithm for discovering over-represented motifs.</p>

<p>For a small set of sequences, such as yours, you could also use Meme, Weeder or others online without installing them locally. Finally, the Regulatory Sequence Analysis Tools (RSAT) ( <a href='http://rsat.ulb.ac.be/rsat/'>http://rsat.ulb.ac.be/rsat/</a> or <a href='http://rsat.ccb.sickkids.ca/'>http://rsat.ccb.sickkids.ca/</a>) are a great place to start for pattern matching and discovery. </p>

<p>In case it is of any use I have put up a short presentation about DNA motif finding from a course I gave earlier this year. You can find it <a href='http://www.slideshare.net/Stewbacca/dna-motif-finding-2010'>here</a>.</p>
