Favorite tool for motif discovery?

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ryan_m
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Favorite tool for motif discovery?

I have some sequences that may or may not contain one or more novel motifs (transcription factor binding sites). I would like to align these using Gibbs sampling or some other technique that will allow me to discover motifs of arbitrary lengths. Are there any experienced power users out there who can suggest some software?

Thanks,

Ryan

bioinfosm
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ryan_m wrote:I have some

ryan_m wrote:

I have some sequences that may or may not contain one or more novel motifs (transcription factor binding sites). I would like to align these using Gibbs sampling or some other technique that will allow me to discover motifs of arbitrary lengths. Are there any experienced power users out there who can suggest some software?

Thanks,

Ryan

MEME might be helpful .. depends on how big your dataset is .. and the amount of noise ! RSAT tools might be useful as well