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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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EMBOSS TRANSFAC转录因子的使用  

2010-08-10 20:00:00|  分类: 生信数据库 |  标签: |举报 |字号 订阅

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主要使用了EMBOSS的2个程序:tfextract, tfscan

http://emboss.sourceforge.net/apps/release/6.2/emboss/apps/tfextract.html


Wiki
The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.


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:6.2.0       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    

 

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-infile]
(Parameter 1)
infile Transfac database sites file Input file Required
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
(none)
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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; Species: 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, 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.  

 

 


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 Processes the PROSITE motif database for use by patmatmotifs
rebaseextract Process the REBASE database for use by restriction enzyme applications

Author(s)
Alan Bleasby (ajb ? ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, 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
None
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