Question: How To Get Consensus Sequence From Motif Id (Or Name)?
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gravatar for anton.kratz
6.2 years ago by
anton.kratz0 wrote:

I have a long list of transcription factor binding motifs, for each motif I have the ID (in a format such as "MA0055.1") and also the name (in a format such as "Myf").

I want to get the consensus sequence (or the degenrated sequence string) for each motif.

Is there any database where I can look this up?

Thanks.

motif • 2.9k views
ADD COMMENTlink modified 6.1 years ago by Biostar ♦♦ 20 • written 6.2 years ago by anton.kratz0
0
gravatar for Alex Reynolds
6.2 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

Sounds like you have JASPAR motifs. Look up your motifs there.

ADD COMMENTlink written 6.2 years ago by Alex Reynolds28k

Hi Alex, yes I have Jaspar motifs. But Jaspar only seems to give me a sequence logo and a frequency matrix. But as written in my question, what I want is the consensus sequence (or the degenrated sequence string) of the motifs.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by anton.kratz0

I'm not sure if I'm missing something about your question, but the sequence logo on the JASPAR site shows the consensus sequence.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Alex Reynolds28k

I already have the sequence logos, but I can not work with them in my programs, they are bitmaps. What I need is the consensus sequence, or degenerated sequence string. (Also I don't need a weight matrix but the consensus sequence string.) For example, given "SF-1" I need to look up that it's "GTCAAGGTCA".

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by anton.kratz0
1

I still do not understand what you're missing. If you have the frequency matrix, you have the consensus sequence: pick the highest frequency base at each position. JASPAR offers freq matrices for its motif calls. A simple script can do this for you, mapping freqs to IUPAC codes. Cf. http://php.scripts.psu.edu/staff/i/u/iua1/theme/media/2011-hershey/what-are-DNA-sequence-motifs.pdf

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Alex Reynolds28k

Okay, I understand. Thanks.

ADD REPLYlink written 6.2 years ago by anton.kratz0
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