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.
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anton.kratz •
Sounds like you have JASPAR motifs. Look up your motifs there.
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.
I'm not sure if I'm missing something about your question, but the sequence logo on the JASPAR site shows the consensus sequence.
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".
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
Okay, I understand. Thanks.
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