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<HTML>
<HEAD>
<TITLE>
EMBOSS: tfextract
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
tfextract
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Extract data from TRANSFAC
<H2>
Description
</H2>
The <A HREF="http://www.gene-regulation.com/pub/databases.html">TRANSFAC
Database</A> is a commercial database of eukaryotic cis-acting
regulatory DNA elements and trans-acting factors. It covers the whole
range from yeast to human.
<p>
An old public domain version is available at:
<a href="ftp://ftp.ebi.ac.uk/pub/databases/transfac/transfac32.tar.Z">
ftp://ftp.ebi.ac.uk/pub/databases/transfac/transfac32.tar.Z</a>
<p>
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:
<p>
<ol>
<li> to guide through a meanwhile overwhelming amount of data in a field
which is connected to nearly all areas of modern molecular biology;
<li> to map the regulatory sites in the individual genes and,
ultimately, in the genome(s) as a whole;
<li> to develop a tool for the identification of regulatory elements in
newly unravelled genomic sequences;
<li> to provide a basis for a more comprehensive understanding of how
the genome governs transcriptional control.
</ol>
<p>
The program <b>tfextract</b> extracts data from the TRANSFAC database
file <b>site.dat</b>. 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.
<p>
The data is split up by taxonomic groups:
<p>
<ul>
<li>Fungi
<li>Insects
<li>Plants
<li>Vertebrates
<li>Other
</ul>
<p>
and placed in individual files:
<p>
<ul>
<li>tffungi
<li>tfinsect
<li>tfplant
<li>tfvertebrate
<li>tfother
</ul>
<p>
These files are stored in the EMBOSS data directory, see <b>Data
Files</b> below.
<H2>
Usage
</H2>
<b>Here is a sample session with tfextract</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>tfextract </b>
Extract data from TRANSFAC
Transfac database sites file: <b>site.dat</b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
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 standard output
-filter boolean Read standard input, write 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. 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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-infile]<br>(Parameter 1)</td>
<td>Transfac database sites file</td>
<td>Input file</td>
<td><b>Required</b></td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
It reads in the TRANSFAC file <b>site.dat</b> available from:
<p>
<!--
<A HREF="http://transfac.gbf.de/cgi-bin/download/download.pl">http://transfac.gbf.de/cgi-bin/download/download.pl</A>
-->
<!--
<A HREF="ftp://transfac.gbf.de/pub/transfac/ascii/old/tf_3.2/transfac32.tar.Z">
ftp://transfac.gbf.de/pub/transfac/ascii/old/tf_3.2/transfac32.tar.Z
-->
<A HREF="ftp://ftp.ebi.ac.uk/pub/databases/transfac/">
ftp://ftp.ebi.ac.uk/pub/databases/transfac/
</A>
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: site.dat</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
AC R00077
XX
ID HS$ALBU_01
XX
DT 20.06.90 (created); ewi.
DT 24.08.95 (updated); hiwi.
XX
TY D
XX
DE albumin; Gene: G000188.
XX
SQ tGGTTAGtaattactaa.
XX
SF -363
ST -338
XX
BF T00368; HNF-1A;Quality: 1; Species: human, Homo sapiens.
BF T00369; HNF-1;Quality: 1; Species: rat, Rattus norvegicus.
BF T01950; HNF-1B;Quality: 1; Species: human, Homo sapiens.
BF T01951; HNF-1C;Quality: 1; Species: human, Homo sapiens.
XX
OS human, Homo sapiens
OC eukaryota; animalia; metazoa; chordata; vertebrata;
OC tetrapoda; mammalia; eutheria; primates
XX
SO 0103; Hep3B
SO 0289; rl
XX
MM gel retardation
MM direct gel shift
MM DNase I footprinting
MM gel shift competition
MM affinity chromatography
MM methylation interference
XX
DR EMBL: M13075; HSALBEX1(695:711).
XX
RN [1]
RA Frain M., Swart G., Monaci P., Nicosia A., Staempfli
RA S., Frank R., Cortese R.
RT The liver-specific transcription factor LF-B1 contains
RT a highly diverged homeobox DNA binding domain
RL Cell 59:145-157 (1989).
RN [2]
RA Frain M., Hardon E., Ciliberto G., Sala-Trepat J. M.
RT Binding of a liver-specific factor to the human albumin
RT gene promoter and enhancer
RL Mol. Cell. Biol. 10:991-999 (1990).
XX
//
<font color=red> [Part of this file has been deleted for brevity]</font>
DR EMBL: U11854; MM11854(1931:1941).
XX
RN [1]
RA Feinman R., Qiu W. Q., Pearse R. N., Nikolajczyk B.
RA S., Sen R., Sheffery M., Ravetch J. V.
RT PU.1 and an HLH family member contribute to the myeloid-specific
RT transcription of the FcgammaRIIIA promoter
RL EMBO J. 13:3852-3860 (1994).
XX
//
AC R04413
XX
ID MOUSE$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
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: tffungi</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
Y$ADH1_02 ACAATATGGACTTCCTCTTTTCTGG R04140 T00322; GCR1;Quality: 2; Species: yeast, Saccharomyces cerevisiae.
</pre>
</td></tr></table><p>
<p><h3>File: tfinsect</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
</pre>
</td></tr></table><p>
<p><h3>File: tfvertebrate</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
HS$ALBU_01 tGGTTAGtaattactaa R00077 T01951; HNF-1C;Quality: 1; Species: human, Homo sapiens.
HS$ALBU_02 TTGGCA R00078 T00599; NF-1/L;Quality: 6; Species: rat, Rattus norvegicus.
HS$ALBU_03 TGGCA R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattus norvegicus.
HS$ALBU_04 TTAATAAT R00080 T00015; AFP1;Quality: 6; Species: human, Homo sapiens.
HS$ALBU_05 TCTAGTTAATAATCTACAAT R00081 T00369; HNF-1;Quality: 4; Species: 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.
</pre>
</td></tr></table><p>
<p><h3>File: tfplant</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
</pre>
</td></tr></table><p>
<p><h3>File: tfother</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
</pre>
</td></tr></table><p>
<p>
The output from tfextract is a set of files in the emboss/data
directory containing reformatted sites from the transfac database.
<p>
These files are used by the tfscan program to search for TRANSFAC sites in
sequences.
<H2>
Data files
</H2>
<p>
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.
<p>
To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
<pre>
% embossdata -fetch -file Exxx.dat
</pre>
<p>
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".
<p>
The directories are searched in the following order:
<ul>
<li> . (your current directory)
<li> .embossdata (under your current directory)
<li> ~/ (your home directory)
<li> ~/.embossdata
</ul>
<p>
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
<ul>
<li>Nucleic Acids Res. 16: 1879-1902, 1988
<li>BioTechForum - Advances in Molecular Genetics (J. Collins,A.J.
Driesel, eds.) 4:95-108, 1991
<li>Nucleic Acids Res. 20:3-26, 1992
</ul>
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with a status of 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="aaindexextract.html">aaindexextract</a></td>
<td>Extract data from AAINDEX</td>
</tr>
<tr>
<td><a href="cutgextract.html">cutgextract</a></td>
<td>Extract data from CUTG</td>
</tr>
<tr>
<td><a href="printsextract.html">printsextract</a></td>
<td>Extract data from PRINTS</td>
</tr>
<tr>
<td><a href="prosextract.html">prosextract</a></td>
<td>Build the PROSITE motif database for use by patmatmotifs</td>
</tr>
<tr>
<td><a href="rebaseextract.html">rebaseextract</a></td>
<td>Extract data from REBASE</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Written Summer 2000 - Alan Bleasby.
<H2>
Target users
</H2>
This program is intended to be used by administrators responsible
for software and database installation and maintenance.
<H2>
Comments
</H2>
None
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</HTML>
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