<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 think this depends on the length of your sequence.
Our MSA editor can add comments to a sequence (manually or from a file), and then a "visual summary" can show 100s of kb in a single picture.
The file format takes motif name, postion, strand, colour for showing these annotations on the sequence.
You can then save this file locally (BBB is Java)
<a href="http://athena.bioc.uvic.ca/virology-ca-tools/base-by-base/">http://athena.bioc.uvic.ca/virology-ca-tools/base-by-base/</a></p>

<p>Hillary, W., S.H. Lin, and C. Upton. 2011.
Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments, BMC Microbial Informatics and Experimentation, 1:2</p>

<p>William Hillary, Song-Han Lin and Chris Upton*</p>

<p>Brodie, R., A.J. Smith, R.L. Roper, V. Tcherepanov, and C. Upton. 2004. 
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments, BMC Bioinformatics, 5, 96.</p>

<p>Cheers,
Chris</p>
