Question: How To Find A Certain Motif Pattern Among Sequences
0
gravatar for dustar1986
8.0 years ago by
dustar1986330
USA
dustar1986330 wrote:

Hi,

I've got a motif pattern, in matrix form. How can I identify if any of a number of sequences contain such a motif ? The motif matix is like: A [ 0 0 0 22 19 55 53 19 9 ] C [ 0 185 185 71 57 44 30 16 78 ] G [185 0 0 46 61 67 91 137 79 ] T [ 0 0 0 46 48 19 11 13 19 ]

And another question: Does anyone know if there is any database that can inquiry RNA polymerase binding motif on DNA? I can only find transcription factor binding motif database on the internet.

Thanks a lot.

motif • 3.0k views
ADD COMMENTlink modified 8.0 years ago by Martin A Hansen3.0k • written 8.0 years ago by dustar1986330
4
gravatar for Alex Reynolds
8.0 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

Take a look at the FIMO portion of the MEME motif discovery suite.

ADD COMMENTlink written 8.0 years ago by Alex Reynolds31k

Thanks a lot, Alex! That's exact what I need.

ADD REPLYlink written 8.0 years ago by dustar1986330
1
gravatar for Martin A Hansen
8.0 years ago by
Martin A Hansen3.0k
Denmark
Martin A Hansen3.0k wrote:

This is exactly what scan_for_matches can do.

ADD COMMENTlink modified 8.0 years ago • written 8.0 years ago by Martin A Hansen3.0k

Thanks. I tried it but it kept saying "failed to parse pattern" when I run it with test DNA motif patterns on my Ubuntu system.

ADD REPLYlink written 8.0 years ago by dustar1986330

If you follow the README carefully it works. PEBKAC :o)

ADD REPLYlink written 8.0 years ago by Martin A Hansen3.0k
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