EMBOSS: tfextract

| ## 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 scop classifications file and writes embl-like format scop classification file
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