Question: Easy matching of a transcription factor binding motif to a DNA promoter sequence
gravatar for secretjess
5.8 years ago by
secretjess180 wrote:

I've been gathering some evidence that several genes are directly regulated by a particular transcription factor I find interesting. I've obtained the transcription factor's binding motif from literature/PAZAR and downloaded sequences 1000 bases to the 5' end of my putative target genes.

Obviously I can (and have) written a regular expression in perl to match occurances of these motifs to my FASTA sequence. But not all of my target genes appear to match my TF's motif in the the sequence I've downloaded. I'm aware of promoter analysis tools (e.g. MEME Suite) but I'm unsure how to use them with the information that I have and I'm not finding the documentation all that helpful (sorry!).

Basically I have:

  • position frequency matrix e.g.

A  [3 3 0 0 0 1 3 0 0 4 0 0 0 4 ]
C  [1 0 2 0 2 2 1 0 0 0 1 0 4 0 ]
G  [0 1 2 0 2 0 0 0 4 0 3 0 0 0 ]
T  [0 0 0 4 0 1 0 4 0 0 0 4 0 0 ]

(or just "TGA[CG]TCA" if that's easier to use/understand)

  • approx. 20 FASTA sequences of promoter region e.g.

>Gene1 promoter



Many thanks for any help/advice

ADD COMMENTlink modified 5.8 years ago by Renesh1.9k • written 5.8 years ago by secretjess180
gravatar for RamRS
5.8 years ago by
Houston, TX
RamRS28k wrote:

I'd use R or Excel to create a probability matrix from the frequency data you have and then use FIMO ( from the web or the command line.

Probability matrix = individual frequency/4 for each position. 

ADD COMMENTlink written 5.8 years ago by RamRS28k

Great! Thank you - I was trying to use FIMO but I didn't know how to generate a motif file. Your answer is really helpful, thanks a lot (P.S. I cannot upvote or accept this answer for some reason)

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by secretjess180
gravatar for Renesh
5.8 years ago by
United States
Renesh1.9k wrote:

First you should use Place and PlantCare databases for identifying motifs in your sequence. After finding the motif in your sequence, you should compare with your list of motifs. The simple regular expression will not help you to find all these motifs.

ADD COMMENTlink written 5.8 years ago by Renesh1.9k
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