Question: Looking For A General Purpose Motif Finder Software
gravatar for anarichardsonsand
8.2 years ago by
anarichardsonsand10 wrote:

Hi! I'm looking for general purpose motif finder software, in the sense that I could input not aligned sequences and get a sequence logo or a PWM or the list of most frequent motifs I've found the cosmo r package

cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy.

But I have problems to find motifs using cosmo in sequences that don't have the 4 nucleotides, are you aware of motifs finders in that sort of sequences?


motif • 3.0k views
ADD COMMENTlink modified 8.2 years ago by Istvan Albert ♦♦ 85k • written 8.2 years ago by anarichardsonsand10

This is very similar to you may find some good pointers there.

ADD REPLYlink written 8.2 years ago by Farhat2.9k
gravatar for Istvan Albert
8.2 years ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

As Farhat put it see Finding common motifs in sequences or TAMO, a framework for analyzing transcriptional regulation using DNA-sequence motifs.

You may also want to search Biostar for word such as motif search

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ADD COMMENTlink modified 8.2 years ago • written 8.2 years ago by Istvan Albert ♦♦ 85k
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