A motif searching program availalbe

Shiping Zhang ping at bnlux1.bnl.gov
Sat Aug 26 23:37:08 EST 1995

In article <lemieuse.809439410 at alize.ERE.UMontreal.CA>,
Lemieux Sebastien <lemieuse at ERE.UMontreal.CA> wrote:
>ping at bnlux1.bnl.gov (Shiping Zhang) writes:
>>A motif searching program is available at the www site
>>It can search GenBank, Swiss-prot or your own DNA/protein sequences
>>for motifs defined in Prosite or defined by yourself.  You can
>>also retrieve entries from Prosite.
>Would it be possible to get an algorithm to find motifs without
>explicitly defining them?  This could be very interesting and really
>helpful [especially in the context of homology 3d modelling].

I'm not sure if you meant to find consensus sequences.  There are
programs doing that.  By definition, the so called motifs are explicitly
defined or discovered patterns, which the program mentioned above
searches in sequences.  One may come up with an algorithm to find motifs.
But an algorithm is actually a set of rules which in turn must be
explicitly defined.


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