                                  tfextract



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Function

   Process TRANSFAC transcription factor database for use by tfscan

Description

   tfextract extracts data from the TRANSFAC transcription factor database
   file site.dat (available from
   ftp://ftp.ebi.ac.uk/pub/databases/transfac/) for other EMBOSS programs,
   such as tfscan, that use these data. The data is split up by taxonomic
   groups and placed in individual files that are stored in the EMBOSS
   data directory.

Usage

   Here is a sample session with tfextract


% tfextract
Process TRANSFAC transcription factor database for use by tfscan
Transfac database sites file: site.dat


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

Command line arguments

Process TRANSFAC transcription factor database for use by tfscan
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     Transfac database sites file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. 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 dying program messages
   -version            boolean    Report version number and exit


Input file format

   It reads in the TRANSFAC file site.dat available from:

   ftp://ftp.ebi.ac.uk/pub/databases/transfac/

  Input files for usage example

  File: 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 T00322; GCR1;Quality: 2; S
pecies: yeast, Saccharomyces cerevisiae.

  File: tfinsect


  File: tfvertebrate

HS$ALBU_01           tGGTTAGtaattactaa R00077 T01951; HNF-1C;Quality: 1; Species
: human, Homo sapiens.
HS$ALBU_02           TTGGCA R00078 T00599; NF-1/L;Quality: 6; Species: rat, Ratt
us norvegicus.
HS$ALBU_03           TGGCA R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattu
s norvegicus.
HS$ALBU_04           TTAATAAT R00080 T00015; AFP1;Quality: 6; Species: human, Ho
mo sapiens.
HS$ALBU_05           TCTAGTTAATAATCTACAAT R00081 T00369; HNF-1;Quality: 4; Speci
es: rat, Rattus norvegicus.
MOUSE$FCGR3A_01      GTCTGCTGACC R04412 T00874; USF;Quality: 2; Species: human,
Homo sapiens.
MOUSE$FCGR3A_02      TTCCTC R04413 T00702; PU.1;Quality: 3; Species: mouse, Mus
musculus.

  File: tfplant


  File: tfother


   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

   The TRANSFAC Database is a commercial database of eukaryotic cis-acting
   regulatory DNA elements and trans-acting factors. It covers the whole
   range from yeast to human. An old public domain version is available
   at: ftp://ftp.ebi.ac.uk/pub/databases/transfac/transfac32.tar.Z

   TRANSFAC started in 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.

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 amino acid property data from AAINDEX
   cutgextract      Extract codon usage tables from CUTG database
   jaspextract      Extract data from JASPAR
   printsextract    Extract data from PRINTS database for use by pscan
   prosextract      Process the PROSITE motif database for use by patmatmotifs
   rebaseextract    Process the REBASE database for use by restriction enzyme
                    applications

Author(s)

   Alan Bleasby
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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

   None
