Searching For A Common Pattern In A Set Of Dna Sequences
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11.3 years ago
Pappu ★ 2.1k

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.

dna • 3.0k views
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11.3 years ago
Neilfws 49k

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

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

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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.

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

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