Motif database

at, Richard T. Timmer timmer at CCWF.CC.UTEXAS.EDU
Mon Jun 8 14:34:55 EST 1992

In Message Mon, 8 Jun 92 13:01:57 -0500,
  danj at (Dan Jacobson x-8453) writes:

>Richard Williams asks:
>>Does anyone know if there are any databases of DNA/protein 'motifs' on
>>the net that I can use to screen sequences for regions of homology with known
>>functional motifs? (- e.g. To scan a protein sequence for potential RNA
>>binding regions). I don't need overall sequence comparison/alignment, but
>>rather a tool to pick out potential regions of interest in sequences of poorly
>>defined function.
>For protein motifs there is PROSITE which can be obatained by anonymous ftp from
>(among other places) in the repository/prosite directory.
>There are two programs which can be used to scan sequences with this database.
>For Unix and Vax/VMS boxes there is prosearch which can be obtained from 
>(among other places) in the molbio/search directory.
>Prosearch is being phased out for PCs.
>For Macs there is Macpattern which is available by anonymous ftp from (among 
>other places) in the MacSciTech/biology directory.
>Kudos to the authors and the ftp sites.
>Best of luck,
>Dan Jacobson
>danj at

Why is Prosearch for PC systems being phased out? Is the nature of the 
database such that the "old" phased-out PC version of Prosearch will not
work with future updates of the PROSITE database?


An feeling abandoned PC user....

Richard Timmer

Dept. of Chem. and Biochem.      (phone)    512-471-4562
The Univ. of Texas at Austin     (fax)      512-471-8696
Austin, TX  78712                (e-mail)   timmer at

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