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
