A request was made for information about a database of transcription
factors. Well this database is called TFD (transcription factor
database) and is available from NCBI. I have included the address of
the ftp site and a listing of the directories which contain tfd files as
well as the readme file for the TFD.
A request was also made for help on archie - since the post was from
Michigan I'll give a US archie site - there are also sites in Canada
(archie's birthplace), Finland, the UK, Israel, Australia ...
To use ARCHIE you may telnet to archie.sura.net and login as archie.
You then can do searches for whatever you want, there is online help. If
you would like I could send you a help file on ARCHIE.
The other (and better) way that you can access archie is with the use of
a prospero client. This allows you to send searches to archie (pipe the
results to a file on your system and put it in background if you'd like),
automatically - no telneting, no fuss - just send it off and read the results
when they come back. To get the client software to do this ftp archie.sura.net
login as anonymous, cd to /pub/archie/client(s?). It's pretty easy to install.
Hope this helps,
Dan Jacobson
danj at jhuhyg.sph.jhu.edu
=============================================================================
=============================================================================
Host ncbi.nlm.nih.gov
Location: /pub/ghosh
FILE -rw-r--r-- 4524948 Oct 16 17:41 tfd.testD.cpt.hqx
FILE -rw-r--r-- 899533 Nov 13 15:30 tfdirx.tar.Z
Location: /repository/TFD/datasets
FILE -rw-r--r-- 847948 Dec 12 18:33 tfdaa
Location: /repository/TFD/tarfiles
FILE -rw-r--r-- 5279327 Jan 27 22:34 tfd.tar.Z
Location: /repository/TFD
DIRECTORY drwxr-xr-x 512 Jan 27 22:19 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 Jan 27 22:21 tfd.asn1
Location: /repository/TFD/tfd.asn1
FILE -rw-r--r-- 7495648 Jan 27 22:22 tfd.asn
FILE -rw-r--r-- 3107 Dec 16 17:14 tfd.asnspec
=========================================================================
================================README===================================
**************************************************************************
* *
* COPYRIGHT NOTICE *
* *
* This software/database is "United States Government Work" under the *
* terms of the United States Copyright Act. It was written as part of *
* the author's official duties as a Government employee and thus cannot *
* be copyrighted. Restrictions cannot be placed on its present or *
* future use. *
* *
* Although all reasonable efforts have been taken to insure the accuracy *
* and reliability of the software and data, the author(s), the National *
* Library of Medicine (NLM) and the U.S. Government do not and cannot *
* warrant the performance or results that may be obtained by using this *
* software or data. The author(s), the NLM and the U.S. Government *
* disclaim all warranties, expressed or implied, as to performance, *
* merchantability or fitness for any particular purpose. *
* *
* In any work or product derived from this material, proper attribution *
* of the author as the source of the software or data would be *
* appreciated. *
* *
**************************************************************************
February 14, 1992
---------------------------------------------------------------------------
I. Release Notes:
This file only contains information specific to the 4.0 and
4.2 releases. Users who are unfamiliar with TFD are suggested
to peruse the contents of README files of previous releases,
which are contained in the "Release-Notes" subdirectory.
II. Number of records per table:
This (4.2) release contains 1658, 929, 434, 1511, and 1887 records
for the clones, domains, factors, polypeptides, and sites tables,
respectively. The methods, n_pointers, references, and x_pointers
tables contain 34, 2552, 5726, and 4872 records respectively.
III. Database structure:
The following changes in database structure have occurred between
releases 3.0 and 4.2:
Table Field Description
---------------------------------------------------------------------------
methods New TFD table containing codes for
experimental methods, corresponding
(in release 4.1) to information
contained in the sites.method field
methods full experimental method
tfdcode two-letter code used by TFD
references medline changed to 'uid'
clones tfd_id changed to 'clone_id'
domains tfd_id changed to 'domain_id'
factors tfd_id changed to 'factor_id'
polypeptides tfd_id changed to 'polypep_id'
sites tfd_id changed to 'site_id'
sites locat_ref new field containing reference point
for coordinates contained in the
sites.location field
n_pointers table1 new field containing the name of the
table for the id referenced in id_1
tfdid1 changed to 'id_1'
table2 new field containing the name of the
table for the id reference in id_2
tfdid2 changed to 'id_2'
x_pointers tfd_table new field containing the name of the
TFD table pointed to in an x_pointers
entry
tfdentry changed to 'tfd_id'
III. Software:
The following public domain software packages can be
used with TFD:
Dynamic, a SITES analysis software tool developed for a UNIX
operating system, which can be obtained from the the MBCRR.
For this product contact Temple Smith (tsmith at darwin.bu.edu).
Signalscan, a SITES analysis software tool developed for use
on a PC, Macintosh, UNIX, or VMS system. For this product
please contact D Presteridge (danp at beagle.colorado.edu).
SITES dataset files for use with these and other software
packages can be found in the directory "datasets".
IV. Reference:
The following references may be consulted for a background
and general description of this database:
Ghosh, D. (1990) A Relational Database of Transcription Factors.
Nucleic Acids Research 18: 1749-1756.
Ghosh, D. (1991) New developments of a Transcription Factors
Database. Trends in Biochemical Sciences 16: 455-457.
V. Help/Further Information:
The following addresses can be used for help requests, mailing
list requests and general questions:
Email (internet) address Purpose
----------------------------------------------------------------------------
tfdhelp at ncbi.nlm.nih.gov TFD-related technical help requests
tfdinfo at ncbi.nlm.nih.gov Address for messages or questions
directed to the TFD users community.
tfdinfo-request at ncbi.nlm.nih.gov Request for subscrtiption to the
TFDINFO users mailing list.
----------------------------------------------------------------------------
David Ghosh
National Center for Biotechnology Information
NLM, NIH
Bethesda, MD 20894 USA
Internet address: ghosh at ncbi.nlm.nih.gov
----------------------------------------------------------------------------
