Motif database

at ccwf.cc.utexas.edu, 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 welchgate.welch.jhu.edu (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) ncbi.nlm.nih.gov 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) ftp.bio.indiana.edu 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) ra.nrl.navy.mil in the MacSciTech/biology directory.
>
>Kudos to the authors and the ftp sites.
>
>Best of luck,
>
>Dan Jacobson
>
>danj at welchgate.welch.jhu.edu

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?

Thanks,

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 ccwf.cc.utexas.edu



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