Motif database

Dan Jacobson x-8453 danj at WELCHGATE.WELCH.JHU.EDU
Mon Jun 8 13:01:57 EST 1992


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

 



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