A motif searching program availalbe

[higgins at ebi.ac.uk]

In article <lemieuse.809439410 at alize.ERE.UMontreal.CA>, lemieuse at ERE.UMontreal.CA (Lemieux Sebastien) writes:
> ping at bnlux1.bnl.gov (Shiping Zhang) writes:
> 
>>A motif searching program is available at the www site
> 
>>http://genome1.bio.bnl.gov/bbq.html
> 
>>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].
> 


If, by this, you mean to find shared patterns in a set of unaligned
sequences, there is a program by Inge Jonassen call Pratt that does this:


Anonymous ftp to:

ftp.ebi.ac.uk


Get the file (binary transfer):

/pub/software/unix/pratt.tar.Z



Des Higgins

EMBL/EBI, Hinxton, UK

> --
> | Sebastien Lemieux, dept. biol.  ||  Look behind the wave of changes
> | lemieuse at alize.ERE.UMontreal.CA ||  Feel the future taking shape
> | PGP public key on finger.       ||  I can see the world to come (KJ)
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