Transcription factor software
Dan Jacobson x-8453
danj at WELCHGATE.WELCH.JHU.EDU
Tue May 19 18:18:29 EST 1992
Mauricio M. Bustos writes:
>I am looking for a program to check new peptide sequences for motifs
>(domains?) characteristic of known transcription factors. For instance, zinc-
>fingers, leucine zippers, helix-loop-helix, homeodomains, POU domains etc.. >It would have to run on VAX/VMS, UNIX or PC machines. Any help at all will be
>greatly appreciated.
Well, there are a few things which you might find usefull. Prosearch will take
a protein and look for known protein motifs by comparing it to the Prosite
database. I believe that you can also use Prosearch to compare a protein to
The TFD (Transcription Factor Database)) - if you use tfd2prosite.c to convert the TFD to Prosite format Of course you may also find the TFD alone to be of use with other comparison software. (There is a Mac version of prosearch called Macpattern too.)
Best of luck,
Dan Jacobson
danj at welchgate.welch.jhu.edu
-------------------------------------------------------------------------------
Prosearch can be found at the following anon-ftp sites:
Host evolution.bchs.uh.edu
Location: /pub/gene-server/incoming
FILE -rw-r--r-- 89761 Apr 9 05:00 prosearch2.0
Location: /pub/gene-server/unix
FILE -rw-r--r-- 89761 Apr 9 05:04 prosearch2.0
FILE -rwxr--r-- 214072 Sep 16 1991 prosearch_1.2.shar
FILE -rwxr--r-- 294983 Sep 16 1991 prosearch_1.2.uue
Location: /pub/gene-server/vms
FILE -rwxr----- 32460 Sep 16 1991 prosearch.shar
FILE -rwxr--r-- 91155 Sep 16 1991 prosearch.uaa
FILE -rwxr--r-- 25524 Sep 16 1991 prosearch.uab
FILE -rwxr--r-- 201069 Sep 16 1991 prosearch12.dclshar
Host fly.bio.indiana.edu
Location: /molbio/search
FILE -rw-r--r-- 61207 May 14 1991 prosearch-vms.com
FILE -rw-r--r-- 4280 May 14 1991 prosearch.readme
FILE -rw-r--r-- 70291 May 14 1991 prosearch.shar
FILE -rw-r--r-- 48697 Mar 23 17:22 prosearch.uue
FILE -rw-r--r-- 89262 Apr 9 12:09 prosearch2.shar
Host mbio.med.upenn.edu
Location: /pub
FILE -rw-r--r-- 82813 Jan 22 1991 ProSearch1.2.shar.Z
FILE -rw-r--r-- 37648 Apr 9 14:27 ProSearch2.0.shar.Z
Host nic.funet.fi
Location: /pub/sci/molbio/unix
FILE -rw-rw-r-- 214072 Jun 17 1991 prosearch_1.2.shar
Location: /pub/sci/molbio/vax
FILE -rw-rw-r-- 201069 Jun 23 1991 prosearch12.dclshar
-------
PROSITE and tfd2prosite.c can be found at the following anon-ftp sites:
Host biox.unibas.ch
Location: /biology/cd
DIRECTORY dr-xr-xr-x 2048 Apr 7 15:20 prosite
Location: /biology/cd/prosite
FILE -r--r--r-- 564040 Mar 26 16:49 prosite.dat
FILE -r--r--r-- 1067471 Mar 26 16:49 prosite.doc
FILE -r--r--r-- 30395 Mar 26 16:49 prosite.lis
FILE -r--r--r-- 32097 Mar 26 16:49 prosite.usr
Location: /biology/database
DIRECTORY drwxr-xr-x 512 Mar 31 07:53 prosite
Location: /biology/database/prosite
FILE -rw-r--r-- 552401 Mar 13 14:11 prosite.dat
FILE -rw-r--r-- 1044660 Mar 13 14:12 prosite.doc
FILE -rw-r--r-- 29731 Mar 13 14:12 prosite.lis
Host evolution.bchs.uh.edu
Location: /pub/gene-server/dos
FILE -rwxr--r-- 11370 Sep 16 1991 tfd2prosite.c
Location: /pub/gene-server/mac
FILE -rwxr--r-- 12307 Mar 3 18:39 tfd2prosite.c
Location: /pub/gene-server/unix
FILE -rwxr--r-- 11371 Sep 16 1991 tfd2prosite.c
Location: /pub/gene-server/vms
FILE -rwxr--r-- 38388 Sep 16 1991 prositec.uue
FILE -rwxr--r-- 11370 Sep 16 1991 tfd2prosite.c
Host fly.bio.indiana.edu
Location: /help/embl
FILE -rw-r--r-- 1261 May 14 1991 prosite.lis
Location: /molbio/data
DIRECTORY drwxr-xr-x 512 Feb 19 23:46 prosite
Location: /molbio/data/prosite
FILE -rw-r--r-- 552411 Feb 19 13:10 prosite.dat
FILE -rw-r--r-- 1044663 Feb 19 13:10 prosite.doc
FILE -rw-r--r-- 29734 Feb 19 13:10 prosite.lis
Location: /molbio/search
FILE -rw-r--r-- 358263 Dec 21 1990 prosite.tar.Z
Host ftp.uni-kl.de
Location: /pub/bio/genbank
FILE -rw-r--r-- 21903 Mar 8 1991 prosite.lis
Host genbank.bio.net
Location: /pub/db
DIRECTORY drwxrwxr-x 512 Jan 26 02:51 prosite
Location: /pub/db/prosite
FILE -rw-r--r-- 552401 Mar 14 10:37 prosite.dat
FILE -rw-r--r-- 1044660 Mar 14 10:38 prosite.doc
FILE -rw-r--r-- 29731 Mar 14 10:38 prosite.lis
Host george.lbl.gov
Location: /pub
FILE -rw-rw-rw- 27101 May 23 1991 ProSite.shar.Z
Host modl.unibas.ch
Location: /biology/database
DIRECTORY drwxr-xr-x 512 Sep 18 1991 prosite
Host ncbi.nlm.nih.gov
Location: /repository/.cdtest
DIRECTORY drwxrwxr-x 512 May 11 15:14 prosite
Location: /repository/.cdtest/prosite
FILE -rwxrwxr-x 552401 May 11 15:14 prosite.dat
FILE -rwxrwxr-x 1044660 May 11 15:14 prosite.doc
FILE -rwxrwxr-x 29731 May 11 15:14 prosite.lis
Location: /repository/blocks/patmat.unix
FILE -rw-r--r-- 198 Feb 29 01:38 prosite.cs
Location: /repository
DIRECTORY drwxr-xr-x 512 Apr 9 17:19 prosite
Location: /repository/prosite
FILE -rw-r--r-- 552401 Mar 13 23:44 prosite.dat
FILE -rw-r--r-- 1044660 Mar 13 23:48 prosite.doc
FILE -rw-r--r-- 29731 Mar 13 23:48 prosite.lis
----------------
The TFD can be found at NCBI:
Host ncbi.nlm.nih.gov
Location: /pub/ghosh
FILE -rw-r--r-- 4524948 Oct 16 00:00 tfd.testD.cpt.hqx
FILE -rw-r--r-- 899533 Nov 13 00:00 tfdirx.tar.Z
Location: /repository/.cdtest
DIRECTORY drwxrwxr-x 512 May 11 21:41 tfd
Location: /repository/.cdtest/tfd/datasets
FILE -rwxrwxr-x 203520 May 11 15:16 TFDSITES.4-0
FILE -rwxrwxr-x 847948 May 11 15:16 tfdaa
Location: /repository/.cdtest/tfd
DIRECTORY drwxrwxr-x 512 May 11 15:18 tfd.asn
Location: /repository/.cdtest/tfd/tfd.asn
FILE -rwxrwxr-x 7497040 May 11 15:18 tfd.asn
FILE -rwxrwxr-x 3107 May 11 15:18 tfd.def
Location: /repository/.cdtest/tfd
DIRECTORY drwxrwxr-x 512 May 11 15:20 tfd.txt
Location: /repository/.cdtest/tfd/tfd.txt
FILE -rwxrwxr-x 3666 May 11 15:20 tfd.dct
Location: /repository
DIRECTORY drwxr-xr-x 512 Apr 26 03:02 TFD
Location: /repository/TFD/datasets
FILE -rw-r--r-- 203520 Dec 16 23:50 TFDSITES.SUBSEQ.4.0
FILE -rw-r--r-- 847948 Dec 12 18:33 tfdaa
Location: /repository/TFD/tarfiles
FILE -rw-r--r-- 5218886 Apr 26 03:00 tfd.tar.Z
Location: /repository/TFD
DIRECTORY drwxr-xr-x 512 Apr 26 02:49 tfd.ascii
Location: /repository/TFD/tfd.ascii
FILE -rw-r--r-- 3666 Dec 12 17:09 tfd.dct
Location: /repository/TFD
DIRECTORY drwxr-xr-x 512 Apr 9 17:17 tfd.asn1
Location: /repository/TFD/tfd.asn1
FILE -rw-r--r-- 7499141 Apr 26 02:51 tfd.asn
FILE -rw-r--r-- 3107 Dec 16 17:14 tfd.asnspec
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