
                                  tfscan 



Function

   Scans DNA sequences for transcription factors

Description

   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

   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

   The program tfscan takes a sequence and the name of one of these
   taxonomic groups and does a fast match of the TRANSFAC sequences
   against the input sequence (optionally allowing mismatches).

   The results is a list of the positions which match the binding sites
   in the TRANSFAC SITE database.

   Because the binding sites are so small, there will be many spurious
   (false positive) matches.

Usage

   Here is a sample session with tfscan


% tfscan 
Scans DNA sequences for transcription factors
Input sequence(s): tembl:hsfos
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 [hsfos.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     Sequence database USA
   -menu               menu       Select class
*  -custom             datafile   Name of data file
   -mismatch           integer    Number of mismatches
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers:
   -minlength          integer    Display matches equal to or above this
                                  length

   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 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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -menu Select class
   F (fungi)
   I (insect)
   P (plant)
   V (vertebrate)
   O (other)
   C (Custom)
   V
   -custom Name of data file Data file File in the data file path
   -mismatch Number of mismatches Integer 0 or more 0
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.tfscan
   Additional (Optional) qualifiers Allowed values Default
   -minlength Display matches equal to or above this length Integer 1 or
   more 1
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   tfscan reads normal nucleic acid sequence USAs.

  Input files for usage example

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

  Database entry: tembl:hsfos

ID   HSFOS      standard; DNA; HUM; 6210 BP.
XX
AC   K00650; M16287;
XX
SV   K00650.1
XX
DT   26-JUL-1991 (Rel. 28, Created)
DT   02-JUL-1999 (Rel. 60, Last updated, Version 3)
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; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-4165
RX   MEDLINE; 83221560.
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   MEDLINE; 86028185.
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   MEDLINE; 87217118.
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   GDB; 119917; FOS.
DR   SWISS-PROT; P01100; FOS_HUMAN.
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.


  [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: hsfos.tfscan

TFSCAN of HSFOS 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

   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

   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

   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 (ableasby © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, 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
