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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