Software for finding amino acid sequences within a protein

[Dan Jacobson]

Prosearch and Macpattern are programs which are designed to find protein motifs
present in your amino acid sequence by comparring it to the prosite database o
f protein motifs.  These programs (I know macpattern will, I'm assuming prosear
ch will too) also allow you to input any sequence you'd like to look for in
your  protein - this should be just the ticket for finding the  site you're
looking for.
    Archie tells me that prosearch, prosite and macpattern are ftp'able from th
e following sites.
==
Happy hunting,

Dan Jacobson
danj at jhuhyg.sph.jhu.edu
=================================Prosearch====================================

Host cs.dal.ca

    Location: /pub/comp.archives
      DIRECTORY drwxrwxrwx        512  Jun 14 03:42  prosearch

Host mbio.med.upenn.edu

    Location: /pub
      DIRECTORY dr-xr-xr-x        512  Jan 22 1991  ProSearch
    Location: /pub/ProSearch
           FILE -rw-r--r--     201069  Jan 22 1991  prosearch12.dclshar
           FILE -rw-r--r--      82813  Jan 22 1991  prosearch_1.2.shar.Z

Host menudo.uh.edu

    Location: /pub/gene-server/unix
           FILE -rw-r--r--     214072  Sep 16 13:17  prosearch_1.2.shar
           FILE -rw-r--r--     294983  Sep 16 13:17  prosearch_1.2.uue
    Location: /pub/gene-server/vms
           FILE -rw-r-----      32460  Sep 16 13:21  prosearch.shar
           FILE -rw-r--r--      91155  Sep 16 13:21  prosearch.uaa
           FILE -rw-r--r--      25524  Sep 16 13:21  prosearch.uab
           FILE -rw-r--r--     201069  Sep 16 13:21  prosearch12.dclshar

Host nic.funet.fi

    Location: /pub/sci/molbio/unix
           FILE -rw-rw-r--     214072  Jun 17 22:11  prosearch_1.2.shar
           FILE -rw-rw-r--     294983  Jun 17 22:13  prosearch_1.2.uue
    Location: /pub/sci/molbio/vax
           FILE -rw-rw-r--     201069  Jun 23 14:30  prosearch12.dclshar

Host srawgw.sra.co.jp

    Location: /.a/sranha/arch/arch/comp.archives/bionet/molbio
      DIRECTORY drwxr-xr-x        512  Jun 14 21:46  prosearch


======================================Prosite==================================

Host cs.dal.ca

    Location: /pub/comp.archives
      DIRECTORY drwxrwxrwx        512  Jan 29 1991  prosite

Host genbank.bio.net

    Location: /pub/db
      DIRECTORY drwxr-xr-x        512  Aug  9 13:50  prosite
    Location: /pub/db/prosite
           FILE -rw-r--r--     467508  Sep  9 12:59  prosite.dat
           FILE -rw-r--r--     866194  Aug 28 08:26  prosite.doc
           FILE -rw-r--r--      25351  Aug 28 08:26  prosite.lis

Host menudo.uh.edu

    Location: /pub/gene-server/dos
           FILE -rw-r--r--      11370  Sep 16 13:13  tfd2prosite.c
    Location: /pub/gene-server/unix
           FILE -rw-r--r--      11371  Sep 16 13:18  tfd2prosite.c
    Location: /pub/gene-server/vms
           FILE -rw-r--r--      38388  Sep 16 13:21  prositec.uue
           FILE -rw-r--r--      11370  Sep 16 13:22  tfd2prosite.c

Host modl.unibas.ch

    Location: /biology/database
      DIRECTORY drwxr-xr-x        512  Jul  5 18:23  prosite
    Location: /biology/database/prosite
           FILE -rw-r--r--     501052  Jul  5 23:19  prosite.dat
           FILE -rw-r--r--     866183  Jul  5 23:23  prosite.doc
           FILE -rw-r--r--      25349  Jul  5 23:22  prosite.lis

Host ncbi.nlm.nih.gov

    Location: /repository
      DIRECTORY drwxr-xr-x        512  May 20 22:13  PROSITE
    Location: /repository/PROSITE
           FILE -rw-r--r--     467508  Sep  9 13:04  prosite.dat
           FILE -rw-r--r--     866194  Aug 27 15:10  prosite.doc
           FILE -rw-r--r--      25351  Aug 27 15:15  prosite.lis

Host srawgw.sra.co.jp

    Location: /.a/sranha/arch/arch/comp.archives/bionet/molbio
      DIRECTORY drwxr-xr-x        512  Jan 30 1991  prosite


==================================Macpattern===================================


Host menudo.uh.edu

    Location: /pub/gene-server/mac
           FILE -rw-r--r--      97223  Sep 16 13:07  macpattern1.hqx
           FILE -rw-r--r--     228430  Sep 16 13:07  macpattern13.hqx
           FILE -rw-r--r--      97307  Sep 16 13:07  macpattern2.hqx
           FILE -rw-r--r--      35639  Sep 16 13:07  macpattern3.hqx

Host nic.funet.fi

    Location: /pub/sci/molbio/mac
           FILE -rw-rw-r--     260963  Jun 23 13:48  macpattern.hqx
           FILE -rw-rw-r--     228146  Jun 27 13:15  macpattern111.hqx
           FILE -rw-rw-r--     188868  Jun 23 13:48  macpattern123.hqx
           FILE -rw-rw-r--     190886  Jun 23 14:12  macpattern124.hqx
           FILE -rw-rw-r--     228430  Jul 19 17:30  macpattern13.hqx

Host ra.nrl.navy.mil

    Location: /MacSciTech/biology
           FILE -rw-rw-rw-     230163  Aug 16 07:21  MacPattern_14.hqx
           FILE -rw-rw-rw-       1696  Aug 16 06:57  MacPattern_14.readme
           FILE -rw-rw-rw-     191809  Jul  2 13:30  macpattern.hqx



I believe that macpattern is also available from the EMBL mail server.