
                                  tfscan 



Function

   Identify transcription factor binding sites in DNA sequences

Description

   tfscan scans one or more DNA sequences for transcription factor
   binding sites from the TRANSFAC database. The taxonomic group (Fungi,
   Insects, ,Plants, Vertebrates or Other) is specified. Matches are
   searched for using fast sequence word-matching, optionally allowing
   mismatches. Because the binding sites are so small, there will be many
   spurious (false positive) matches. Optionally, the minimum length of a
   match to be reported may be specified.

   An output file is written with information on the matches, including
   sequence ID and accession number, the start and end positions of the
   match in an input sequence and the sequence of the region where a
   match has been found. Binding factor information, where available, is
   given at the end of the matches for each matching entry.

Usage

   Here is a sample session with tfscan


% tfscan 
Identify transcription factor binding sites in DNA sequences
Input nucleotide sequence(s): tembl:k00650
Transcription Factor Class
         F : fungi
         I : insect
         P : plant
         V : vertebrate
         O : other
         C : Custom
Select class [V]: v
Number of mismatches [0]: 
Output file [k00650.tfscan]: 

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

Command line arguments

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -menu               menu       [V] Select class (Values: F (fungi); I
                                  (insect); P (plant); V (vertebrate); O
                                  (other); C (Custom))
*  -custom             datafile   Transfac database data file (optional)
   -mismatch           integer    [0] Number of mismatches (Integer 0 or more)
  [-outfile]           outfile    [*.tfscan] Output file name

   Additional (Optional) qualifiers:
   -minlength          integer    [1] Display matches equal to or above this
                                  length (Integer 1 or more)

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   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. 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

Input file format

   tfscan reads normal nucleic acid sequence USAs.

  Input files for usage example

   'tembl:k00650' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:k00650

ID   K00650; SV 1; linear; genomic DNA; STD; HUM; 6210 BP.
XX
AC   K00650; M16287;
XX
DT   26-JUL-1991 (Rel. 28, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 4)
XX
DE   Human fos proto-oncogene (c-fos), complete cds.
XX
KW   c-myc proto-oncogene; fos oncogene; proto-oncogene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-4165
RX   PUBMED; 6574479.
RA   van Straaten F., Muller R., Curran T., Van Beveren C., Verma I.M.;
RT   "Complete nucleotide sequence of a human c-onc gene: deduced amino acid
RT   sequence of the human c-fos protein";
RL   Proc. Natl. Acad. Sci. U.S.A. 80(11):3183-3187(1983).
XX
RN   [2]
RX   DOI; 10.1016/0092-8674(85)90285-5.
RX   PUBMED; 2414012.
RA   Treisman R.;
RT   "Transient accumulation of c-fos RNA following serum stimulation requires
a
RT   conserved 5' element and c-fos 3' sequences";
RL   Cell 42(3):889-902(1985).
XX
RN   [3]
RP   4166-6210
RX   PUBMED; 3555978.
RA   Verma I.M., Deschamps J., Van Beveren C., Sassone-Corsi P.;
RT   "Human fos gene";
RL   Cold Spring Harb. Symp. Quant. Biol. 51:0-0(0).
XX
DR   EPD; EP11145; HS_FOS.
DR   TRANSFAC; R00458; HS$CFOS_01.
DR   TRANSFAC; R00459; HS$CFOS_02.
DR   TRANSFAC; R00460; HS$CFOS_03.
DR   TRANSFAC; R00461; HS$CFOS_04.
DR   TRANSFAC; R00463; HS$CFOS_06.
DR   TRANSFAC; R00464; HS$CFOS_07.
DR   TRANSFAC; R00465; HS$CFOS_08.
DR   TRANSFAC; R00466; HS$CFOS_09.
DR   TRANSFAC; R00467; HS$CFOS_10.
DR   TRANSFAC; R00468; HS$CFOS_11.


  [Part of this file has been deleted for brevity]

     ccagctgtgc agctgcccac cgcaagggca gcagcagcaa tgagccttcc tctgactcgc      330
0
     tcagctcacc cacgctgctg gccctgtgag ggggcaggga aggggaggca gccggcaccc      336
0
     acaagtgcca ctgcccgagc tggtgcatta cagagaggag aaacacatct tccctagagg      342
0
     gttcctgtag acctagggag gaccttatct gtgcgtgaaa cacaccaggc tgtgggcctc      348
0
     aaggacttga aagcatccat gtgtggactc aagtccttac ctcttccgga gatgtagcaa      354
0
     aacgcatgga gtgtgtattg ttcccagtga cacttcagag agctggtagt tagtagcatg      360
0
     ttgagccagg cctgggtctg tgtctctttt ctctttctcc ttagtcttct catagcatta      366
0
     actaatctat tgggttcatt attggaatta acctggtgct ggatattttc aaattgtatc      372
0
     tagtgcagct gattttaaca ataactactg tgttcctggc aatagtgtgt tctgattaga      378
0
     aatgaccaat attatactaa gaaaagatac gactttattt tctggtagat agaaataaat      384
0
     agctatatcc atgtactgta gtttttcttc aacatcaatg ttcattgtaa tgttactgat      390
0
     catgcattgt tgaggtggtc tgaatgttct gacattaaca gttttccatg aaaacgtttt      396
0
     attgtgtttt taatttattt attaagatgg attctcagat atttatattt ttattttatt      402
0
     tttttctacc ttgaggtctt ttgacatgtg gaaagtgaat ttgaatgaaa aatttaagca      408
0
     ttgtttgctt attgttccaa gacattgtca ataaaagcat ttaagttgaa tgcgaccaac      414
0
     cttgtgctct tttcattctg gaagtcttgt aagtttctga aaggtattat tggagaccag      420
0
     tttgtcaaga agggtagctg ctggaggggg acacaccctc tgtctgatcc cttatcaaag      426
0
     aggacaagga aactatagag ctgattttag aatattttac aaatacatgc cttccattgg      432
0
     aatgctaaga ttttctactg cttctgggga cgggaaaccg ctgtgtaaca gcttttgtgg      438
0
     gaatacattt tttctgtttc agtactcgca gggggaaata tttaaatttt gttgtgctaa      444
0
     tattaaattc agatgttttg atcttaaagg aaccctttaa gcaaacagaa cctagctttg      450
0
     tacagactat tttaactttt tattctcaca aaatcacgtg gagggttatt ctacttcaaa      456
0
     gatgagcaaa ttgaagaatg gttagaataa acaactttct tgatattccg ttatcggcat      462
0
     tagaatcttc ctgctcgtta tcgtatccag caggctgaac tgcctcttga tacttggtta      468
0
     aaaaaaattt tcaggccggg cgcggtggcc catgcctgta atcctagcac tttgggaggc      474
0
     cgaggcaggc ggatcacctg aggtcgggag ttcgagacca gcctgaccaa catggagaaa      480
0
     ccccgtcttt actaaaaata caaaattagc ctggtgtggt ggtgcatgcc tgtaatccta      486
0
     gctacttgag aggctgagac aggaaaatca cttgaactcg ggaggcggat gttgcagcga      492
0
     actgagattg cgccattgca ctccagcctg ggcaacaaga ttgaaactct gtttaaaaaa      498
0
     aaaagttttc actaatgtgt acattttttt gtactctttt attctcgaaa gggaaggagg      504
0
     gctattgccc tatcccttat taataaatgc attgtggttt ctggtttctc taataccata      510
0
     tgcccttcat tcagtttata gtgggcggaa gtgggggaga aaaagttgct cagaaatcaa      516
0
     aagatatctc aaacagcaca aataatggct gatcgttctg caaacaaaaa gttacataat      522
0
     agctcaagaa ggagaagtca acatgactct gaacaagctt taacttagaa actttatcat      528
0
     cttaaggaag aacgtgacct ttgtccagga cgtctctggt aatggggcac ttacacacac      534
0
     atgcacacgt acaaaccaca gggaaaggag accgcccttc tgcctctgct cgcgagtatc      540
0
     acgcaggcac catgcactat gttttcacac acactgggtg gaagaagagc ttcagcgcca      546
0
     gtcttctaat gctttggtga taatgaaaat cactgggtgc ttatggggtg tcatattcaa      552
0
     tcgagttaaa agttttaatt caaaatgaca gttttactga ggttgatgtt ctcgtctatg      558
0
     atatctctgc ccctcccata aaaatggaca tttaaaagca acttaccgct ctttagatca      564
0
     ctcctatatc acacaccact tggggtgctg tttctgctag acttgtgatg acagtggcct      570
0
     taggatccct gtttgctgtt caaagggcaa atattttata gcctttaaat atacctaaac      576
0
     taaatacaga attaatataa ctaacaaaca cctggtctga aataacaagg tgatctaccc      582
0
     tggaaggaac ccagctggtg ggccaggagc ggtggctcac acctgtaatt ccagcacttt      588
0
     gggaggctga gacaggagga tcactggagt ccaggagttt gagaccagcc tgggcaacat      594
0
     ggcaaaaccc agtgtgcttc tgttgtccca gctacactac tcaggaggct gaggcaggag      600
0
     tatgacttga gcctgggagg gggaggttgc agagaactga tattgcacca ccactgcact      606
0
     ccagcctggg tgacacagca aaaccctatc tcaaaaaaaa aaaaaaaaaa aaggaaccca      612
0
     gctggttcct gtaggtgtgc aataataaca accagaggaa gaaaaggaag acgatttccc      618
0
     agatgaagaa gggcagctgg accttcggac                                       621
0
//

Output file format

  Output files for usage example

  File: k00650.tfscan

TFSCAN of K00650 from 1 to 6210

MOUSE$FCGR3A_02      R04413   3287  3292  ttcctc
                     T00702; PU.1;Quality: 3; Species: mouse, Mus musculus.
HS$ALBU_03           R00079   5940  5944  tggca
HS$ALBU_03           R00079   3757  3761  tggca
HS$ALBU_03           R00079   2776  2780  tggca
HS$ALBU_03           R00079   2418  2422  tggca
HS$ALBU_03           R00079   2010  2014  tggca
HS$ALBU_03           R00079   1676  1680  tggca
HS$ALBU_03           R00079   1356  1360  tggca
                     T00599; NF-1/L;Quality: 6; Species: rat, Rattus norvegicus
.
HS$ALBU_02           R00078   2009  2014  ttggca

   The output consists of a title line then 5 columns separated by
   whitespace.

   The first column is the identifier of the entry.

   The second column is the Accession Number of the entry.

   The third and fourth columns are the start and end positions of the
   match in your input sequence.

   The fifth column is the sequence of the region where a match has been
   found.

   Binding factor information, where available, is given at the end of
   the matches for each matching entry.

Data files

   tfscan reads the TRANSFAC SITE data held in the EMBOSS data files:

     * tffungi
     * tfinsect
     * tfplant
     * tfvertebrate
     * tfother

   Your EMBOSS administrator will have to run the EMBOSS program
   tfextract in order to set these files up from the TRANSFAC
   distribution 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. The site.dat data file from
   TRANSFAC contains information on individual (putatively) regulatory
   protein binding sites. It has been divided into the following
   taxonomic groups.
     * Fungi
     * Insects
     * Plants
     * Vertebrates
     * Other

   An old public domain version of TRANSFAC is available at:
   ftp://ftp.ebi.ac.uk/pub/databases/transfac/transfac32.tar.Z

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

   Your EMBOSS administrator will have to run the EMBOSS program
   tfextract in order to set up the data files from the TRANSFAC
   distribution files.

Diagnostic Error Messages

   "EMBOSS An error in tfscan.c at line 82:
   Either EMBOSS_DATA undefined or TFEXTRACT needs running"

   This means that you should contact your EMBOSS administrator and ask
   them to run the tfextract program to set up the TRANSFAC data for
   EMBOSS.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name                  Description
   jaspscan     Scans DNA sequences for transcription factors

   Your EMBOSS administrator will have to run the EMBOSS program
   tfextract in order to set up the data files from the TRANSFAC
   distribution files.

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 everyone and everything, from
   naive users to embedded scripts.

Comments

   None
