<p>I have few motifs whose location on a given DNA sequence has been identified using MATCH (from TRANSFAC). MATCH provides the location of these matrices in a numerical way as motif 1  236 (+) (for an example - motif 1 is present at location 236). I want to get a graphical output by feeding the length of DNA sequence and the the position of matrices so that its easy for presentation and comparing two different sequences with almost similar motifs</p>

<p>Thanks in advance for any suggestions</p>

<p>I always liked Melina II for graphical display of the features on the sequence, and it gives a sequence logo as well. <a href="http://melina2.hgc.jp/public/index.html">http://melina2.hgc.jp/public/index.html</a> But if your motifs aren't identified with the selected tools they offer for "methods" I don't know if it would work for you.</p>
