Looking For A General Purpose Motif Finder Software

Question

[anarichardsonsand]

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

http://www.bioconductor.org/packages/2.10/bioc/html/cosmo.html

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?

Ana

[Farhat]

This is very similar to http://www.biostars.org/post/show/4/finding-common-motifs-in-sequences/ you may find some good pointers there.

Answer 1

[Istvan Albert]

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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