What’s the answer? (graphical motif display)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question is one that I see pretty often. Someone needs a small tool that helps to display their motif features on a sequence:

Represent motifs on a DNA sequence in a graphical way

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

Thanks in advance for any suggestions

novino11

This is actually something that I’ve highlighted several times on the blog. Although this question focuses on DNA motifs, we see it also for protein domains on sequences too. Frequently people would like some tool (besides powerpoint) that does proportional, appropriately positioned, and simple visuals for their presentations or publications. The last time I pulled my posts on these types of tools together I focused on FancyGene, but you’ll see that I reference and link to details about the others in the piece as well.

If you have other tools that you know that could assist with this, let us know–we love to highlight them. And answer over at BioStars.

2 thoughts on “What’s the answer? (graphical motif display)

  1. Mary Post author

    Thanks Christian–sounds good. I hope you can put a web interface together–maybe put that in an upcoming grant. I think there’s a real need for these types of tools.

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