How To Find A Certain Motif Pattern Among Sequences

Question

[dustar1986]

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.

Answer 1

[Alex Reynolds]

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

[dustar1986]

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

Answer 2

[Martin A Hansen]

This is exactly what scan_for_matches can do.

[dustar1986]

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.

[Martin A Hansen]

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