| 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/site.dat

Go to the input files for this example
Go to the output files for this example

## Command line arguments

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

       Optional qualifiers: (none)
       Advanced qualifiers: (none)
       Associated qualifiers: (none)
       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -verbose             boolean    Report some/full command line options
       -help                boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning             boolean    Report warnings
       -error               boolean    Report errors
       -fatal               boolean    Report fatal errors
       -die                 boolean    Report deaths

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:

ftp://transfac.gbf.de/pub/transfac/ascii/old/tf_3.2/transfac32.tar.Z

### Input files for usage example

### File: ../../data/site.dat

    AC  R00077
    XX
    ID  HS$ALBU_01
    XX
    DT  20.06.90 (created); ewi.
    DT  24.08.95 (updated); hiwi.
    XX
    TY  D
    XX
    DE  albumin; Gene: G000188.
    XX
    SQ  tGGTTAGtaattactaa.
    XX
    SF  -363
    ST  -338
    XX
    BF  T00368; HNF-1A;Quality: 1; Species: human, Homo sapiens.
    BF  T00369; HNF-1;Quality: 1; Species: rat, Rattus norvegicus.
    BF  T01950; HNF-1B;Quality: 1; Species: human, Homo sapiens.
    BF  T01951; HNF-1C;Quality: 1; Species: human, Homo sapiens.
    XX
    OS  human, Homo sapiens
    OC  eukaryota; animalia; metazoa; chordata; vertebrata;
    OC  tetrapoda; mammalia; eutheria; primates
    XX
    SO  0103; Hep3B
    SO  0289; rl
    XX
    MM  gel retardation
    MM  direct gel shift
    MM  DNase I footprinting
    MM  gel shift competition
    MM  affinity chromatography
    MM  methylation interference
    XX
    DR  EMBL: M13075; HSALBEX1(695:711).
    XX
    RN  [1]
    RA  Frain M., Swart G., Monaci P., Nicosia A., Staempfli
    RA  S., Frank R., Cortese R.
    RT  The liver-specific transcription factor LF-B1 contains
    RT  a highly diverged homeobox DNA binding domain
    RL  Cell 59:145-157 (1989).
    RN  [2]
    RA  Frain M., Hardon E., Ciliberto G., Sala-Trepat J. M.
    RT  Binding of a liver-specific factor to the human albumin
    RT  gene promoter and enhancer
    RL  Mol. Cell. Biol. 10:991-999 (1990).
    XX
    //

      [Part of this file has been deleted for brevity]

    DR  EMBL: U11854; MM11854(1931:1941).
    XX
    RN  [1]
    RA  Feinman R., Qiu W. Q., Pearse R. N., Nikolajczyk B.
    RA  S., Sen R., Sheffery M., Ravetch J. V.
    RT  PU.1 and an HLH family member contribute to the myeloid-specific
    RT  transcription of the FcgammaRIIIA promoter
    RL  EMBO J. 13:3852-3860 (1994).
    XX
    //
    AC  R04413
    XX
    ID  MOUSE$FCGR3A_02
    XX
    DT  14.05.97 (created); ewi.
    DT  14.05.97 (updated); ewi.
    XX
    TY  D
    XX
    DE  FcgammaRIIIA (low-affinity Fc receptor IIIA for IgG); Gene: G001014.
    XX
    SQ  TTCCTC.
    XX
    EL  MRR
    XX
    SF  -48
    ST  -43
    XX
    BF  T00702; PU.1;Quality: 3; Species: mouse, Mus musculus.
    XX
    OS  mouse, Mus musculus
    OC  eukaryota; animalia; metazoa; chordata; vertebrata;
    OC  tetrapoda; mammalia; eutheria; rodentia; myomorpha; muridae; murinae
    XX
    SO  0495; A20
    SO  0848; RAW264.7
    XX
    MM  direct gel shift
    MM  methylation interference
    MM  supershift (antibody binding)
    XX
    DR  EMBL: U11854; MM11854(1971:1976).
    XX
    RN  [1]
    RA  Feinman R., Qiu W. Q., Pearse R. N., Nikolajczyk B.
    RA  S., Sen R., Sheffery M., Ravetch J. V.
    RT  PU.1 and an HLH family member contribute to the myeloid-specific
    RT  transcription of the FcgammaRIIIA promoter
    RL  EMBO J. 13:3852-3860 (1994).
    XX
    //

## Output file format

### Output files for usage example

### File: tffungi

    Y$ADH1_02            ACAATATGGACTTCCTCTTTTCTGG R04140

### File: tfinsect

### File: tfother

### File: tfplant

### File: tfvertebrate

    HS$ALBU_01           tGGTTAGtaattactaa R00077
    HS$ALBU_02           TTGGCA R00078
    HS$ALBU_03           TGGCA R00079
    HS$ALBU_04           TTAATAAT R00080
    HS$ALBU_05           TCTAGTTAATAATCTACAAT R00081
    MOUSE$FCGR3A_01      GTCTGCTGACC R04412
    MOUSE$FCGR3A_02      TTCCTC R04413

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.

## 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
--- | ---
aaindexextract | Extract data from AAINDEX
cutgextract | Extract data from CUTG
printsextract | Extract data from PRINTS
prosextract | Builds the PROSITE motif database for patmatmotifs to search
rebaseextract | Extract data from REBASE

## Author(s)

Alan Bleasby (ableasby © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, 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