Searching For A Common Pattern In A Set Of Dna Sequences

Question

[Pappu]

I have a set of non-coding DNA sequences which are few hundred base pairs in length. They probably have a repeated set of common motifs or inverted repeats or other similar patters, since same family of proteins bind to them. I aligned them using clustal omega and mummer. However the DNA sequences don't have much in common. I am wondering what is way to go. Thank you.

Answer 1

[Neilfws]

One or more of the tools in the MEME suite is the way to go.

[Martin A Hansen]

Hah, we posted the same suggestion simultaneously. Yours did show up first, so I deleted mine.

[Pappu]

Thank you guys. Iinitial results from MEME looks good. I saw it before but did not try because there are so many of them. I think it is the best to ask someone who is the field for a while which tools are good.

[Erik Garrison]

I've had great success with tools in the MEME suite. I particularly like the HTML output.