Question: Easy matching of a transcription factor binding motif to a DNA promoter sequence
0
gravatar for secretjess
5.0 years ago by
secretjess170
Cambridge
secretjess170 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

ATGCATGCATGCATGCATGCATGCATGCATGC(...to a total of 1000 bases)

 

Many thanks for any help/advice

ADD COMMENTlink modified 5.0 years ago by Renesh1.6k • written 5.0 years ago by secretjess170
2
gravatar for RamRS
5.0 years ago by
RamRS24k
Houston, TX
RamRS24k wrote:

I'd use R or Excel to create a probability matrix from the frequency data you have and then use FIMO (http://meme.nbcr.net/meme/fimo-intro.html) from the web or the command line.

Probability matrix = individual frequency/4 for each position. 

ADD COMMENTlink written 5.0 years ago by RamRS24k
1

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 5.0 years ago • written 5.0 years ago by secretjess170
0
gravatar for Renesh
5.0 years ago by
Renesh1.6k
United States
Renesh1.6k wrote:

First you should use Place http://www.dna.affrc.go.jp/PLACE/ and PlantCare http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ 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 5.0 years ago by Renesh1.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2076 users visited in the last hour