
                             EMBOSS: tfextract
     _________________________________________________________________
   
                               Program tfextract
                                       
Function

   Extract data from TRANSFAC
   
Description

   The TRANSFAC Database is a database of eukaryotic cis-acting
   regulatory DNA elements and trans-acting factors. It covers the whole
   range from yeast to human.
   
   TRANSFAC started 1988 with a printed compilation (Nucleic Acids Res.
   16: 1879-1902, 1988) and was transferred into computer-readable format
   in 1990 (BioTechForum - Advances in Molecular Genetics (J. Collins,
   A.J. Driesel, eds.) 4:95-108, 1991). The basic structures of Table 1
   and 2 of the compilation were taken as the core of the emergent
   database. The aim of the early compilation as well as of the TRANSFAC
   database is
   
    1. to guide through a meanwhile overwhelming amount of data in a
       field which is connected to nearly all areas of modern molecular
       biology;
    2. to map the regulatory sites in the individual genes and,
       ultimately, in the genome(s) as a whole;
    3. to develop a tool for the identification of regulatory elements in
       newly unravelled genomic sequences;
    4. to provide a basis for a more comprehensive understanding of how
       the genome governs transcriptional control.
       
   The program tfextract extracts data from the TRANSFAC database file
   site.dat. This file contains information on individual (putatively)
   regulatory protein binding sites. About half of these refer to sites
   within eukaryotic genes. Just under half of them resulted from
   mutagenesis studies, in vitro selection procedures starting from
   random oligonucleotide mixtures or from specific theoretical
   considerations. And finally, there are about 5% with consensus binding
   sequences given in the IUPAC code, many of them being taken from the
   compilation of Faisst and Meyer (Nucleic Acids Res. 20:3-26, 1992). A
   number of consensi have been generated by the TRANSFAC team, generally
   derived from the profiles stored in the MATRIX table.
   
   The data is split up by taxonomic groups:
   
     * Fungi
     * Insects
     * Plants
     * Vertebrates
     * Other
       
   and placed in individual files:
   
     * tffungi
     * tfinsect
     * tfplant
     * tfvertebrate
     * tfother
       
   These files are stored in the EMBOSS data directory, see Data Files
   below.
   
Usage

   Here is a sample session with tfextract.

% tfextract
Extract data from TRANSFAC
Full pathname of transfac SITE.DAT: /data/transfac/site.dat

Command line arguments

   Mandatory qualifiers:
  [-inf]               infile     Full pathname of transfac SITE.DAT

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-inf]
   (Parameter 1) Full pathname of transfac SITE.DAT Input file Required
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   It reads in the TRANSFAC file site.dat distributed from the TRANSFAC
   site:
   
   http://transfac.gbf.de/cgi-bin/download/download.pl
   
Output file format

   The output from tfextract is a set of files in the emboss/data
   directory containing reformatted sites from the transfac database.
   
   These files are used by the tfscan program to search for TRANSFAC
   sites in sequences.

% ls -1s emboss/data/tf*
 18 emboss/data/tffungi
 17 emboss/data/tfinsect
 56 emboss/data/tfother
  4 emboss/data/tfplant
112 emboss/data/tfvertebrate

Data files

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.
   
   To see the available EMBOSS data files, run:
   
% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".
   
   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata
       
Notes

   None.
   
References

     * Nucleic Acids Res. 16: 1879-1902, 1988
     * BioTechForum - Advances in Molecular Genetics (J. Collins,A.J.
       Driesel, eds.) 4:95-108, 1991
     * Nucleic Acids Res. 20:3-26, 1992
       
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with a status of 0.
   
Known bugs

   None.
   
See also

   Program name Description
   cutgextract Extract data from CUTG
   domainer Build domain coordinate files
   nrscope Converts redundant EMBL-format SCOP file to non-redundant one
   pdbtosp Convert raw swissprot:pdb equivalence file to embl-like format
   printsextract Extract data from PRINTS
   prosextract Builds the PROSITE motif database for patmatmotifs to
   search
   rebaseextract Extract data from REBASE
   scope Convert raw scop classification file to embl-like format
   scopparse Reads raw-, and writes EMBL-like, scop classification files
   seqnr Converts redundant database results to a non-redundant set of
   hits
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

   Written Summer 2000 - Alan Bleasby.
   
Target users

   This program is intended to be used by administrators responsible for
   software and database installation and maintenance.
   
Comments
