Question: Searching For A Common Pattern In A Set Of Dna Sequences
1
gravatar for Pappu
7.4 years ago by
Pappu1.9k
Pappu1.9k wrote:

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 • 2.2k views
ADD COMMENTlink modified 7.4 years ago by Martin A Hansen3.0k • written 7.4 years ago by Pappu1.9k
6
gravatar for Neilfws
7.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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

ADD COMMENTlink written 7.4 years ago by Neilfws48k

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

ADD REPLYlink written 7.4 years ago by Martin A Hansen3.0k

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.

ADD REPLYlink written 7.4 years ago by Pappu1.9k

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

ADD REPLYlink written 7.4 years ago by Erik Garrison2.3k
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