tfscan 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 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 report [k00650.tfscan]: Go to the input files for this example Go to the output files for this example Command line arguments Identify transcription factor binding sites in DNA sequences Version: EMBOSS:6.4.0.0 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] report [*.tfscan] Output report file name (default -rformat seqtable) 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 -rformat2 string Report format -rname2 string Base file name -rextension2 string File name extension -rdirectory2 string Output directory -raccshow2 boolean Show accession number in the report -rdesshow2 boolean Show description in the report -rscoreshow2 boolean Show the score in the report -rstrandshow2 boolean Show the nucleotide strand in the report -rusashow2 boolean Show the full USA in the report -rmaxall2 integer Maximum total hits to report -rmaxseq2 integer Maximum hits to report for one sequence 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 tfscan reads one or more nucleotide sequences. The input is a standard EMBOSS sequence query (also known as a 'USA'). Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application. The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. 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 DOI; 10.1073/pnas.80.11.3183. 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. XX CC [2] sites; promoter region. CC C-fos is the human cellular homolog of the v-fos oncogene of CC Finkel-Biskis-Jinkins murine osteosarcoma virus (FBJ-MuSV). [2] It CC was found that both human and murine c-fos genes contained an CC enhancer-like element in their 5' noncoding regions that was CC necessary for increased transcription following serum activation. CC The FBJ-MuSV v-fos oncogene contains a deletion relative to murine CC and human c-fos proto-oncogenes that causes complete divergence of [Part of this file has been deleted for brevity] ccagctgtgc agctgcccac cgcaagggca gcagcagcaa tgagccttcc tctgactcgc 3300 tcagctcacc cacgctgctg gccctgtgag ggggcaggga aggggaggca gccggcaccc 3360 acaagtgcca ctgcccgagc tggtgcatta cagagaggag aaacacatct tccctagagg 3420 gttcctgtag acctagggag gaccttatct gtgcgtgaaa cacaccaggc tgtgggcctc 3480 aaggacttga aagcatccat gtgtggactc aagtccttac ctcttccgga gatgtagcaa 3540 aacgcatgga gtgtgtattg ttcccagtga cacttcagag agctggtagt tagtagcatg 3600 ttgagccagg cctgggtctg tgtctctttt ctctttctcc ttagtcttct catagcatta 3660 actaatctat tgggttcatt attggaatta acctggtgct ggatattttc aaattgtatc 3720 tagtgcagct gattttaaca ataactactg tgttcctggc aatagtgtgt tctgattaga 3780 aatgaccaat attatactaa gaaaagatac gactttattt tctggtagat agaaataaat 3840 agctatatcc atgtactgta gtttttcttc aacatcaatg ttcattgtaa tgttactgat 3900 catgcattgt tgaggtggtc tgaatgttct gacattaaca gttttccatg aaaacgtttt 3960 attgtgtttt taatttattt attaagatgg attctcagat atttatattt ttattttatt 4020 tttttctacc ttgaggtctt ttgacatgtg gaaagtgaat ttgaatgaaa aatttaagca 4080 ttgtttgctt attgttccaa gacattgtca ataaaagcat ttaagttgaa tgcgaccaac 4140 cttgtgctct tttcattctg gaagtcttgt aagtttctga aaggtattat tggagaccag 4200 tttgtcaaga agggtagctg ctggaggggg acacaccctc tgtctgatcc cttatcaaag 4260 aggacaagga aactatagag ctgattttag aatattttac aaatacatgc cttccattgg 4320 aatgctaaga ttttctactg cttctgggga cgggaaaccg ctgtgtaaca gcttttgtgg 4380 gaatacattt tttctgtttc agtactcgca gggggaaata tttaaatttt gttgtgctaa 4440 tattaaattc agatgttttg atcttaaagg aaccctttaa gcaaacagaa cctagctttg 4500 tacagactat tttaactttt tattctcaca aaatcacgtg gagggttatt ctacttcaaa 4560 gatgagcaaa ttgaagaatg gttagaataa acaactttct tgatattccg ttatcggcat 4620 tagaatcttc ctgctcgtta tcgtatccag caggctgaac tgcctcttga tacttggtta 4680 aaaaaaattt tcaggccggg cgcggtggcc catgcctgta atcctagcac tttgggaggc 4740 cgaggcaggc ggatcacctg aggtcgggag ttcgagacca gcctgaccaa catggagaaa 4800 ccccgtcttt actaaaaata caaaattagc ctggtgtggt ggtgcatgcc tgtaatccta 4860 gctacttgag aggctgagac aggaaaatca cttgaactcg ggaggcggat gttgcagcga 4920 actgagattg cgccattgca ctccagcctg ggcaacaaga ttgaaactct gtttaaaaaa 4980 aaaagttttc actaatgtgt acattttttt gtactctttt attctcgaaa gggaaggagg 5040 gctattgccc tatcccttat taataaatgc attgtggttt ctggtttctc taataccata 5100 tgcccttcat tcagtttata gtgggcggaa gtgggggaga aaaagttgct cagaaatcaa 5160 aagatatctc aaacagcaca aataatggct gatcgttctg caaacaaaaa gttacataat 5220 agctcaagaa ggagaagtca acatgactct gaacaagctt taacttagaa actttatcat 5280 cttaaggaag aacgtgacct ttgtccagga cgtctctggt aatggggcac ttacacacac 5340 atgcacacgt acaaaccaca gggaaaggag accgcccttc tgcctctgct cgcgagtatc 5400 acgcaggcac catgcactat gttttcacac acactgggtg gaagaagagc ttcagcgcca 5460 gtcttctaat gctttggtga taatgaaaat cactgggtgc ttatggggtg tcatattcaa 5520 tcgagttaaa agttttaatt caaaatgaca gttttactga ggttgatgtt ctcgtctatg 5580 atatctctgc ccctcccata aaaatggaca tttaaaagca acttaccgct ctttagatca 5640 ctcctatatc acacaccact tggggtgctg tttctgctag acttgtgatg acagtggcct 5700 taggatccct gtttgctgtt caaagggcaa atattttata gcctttaaat atacctaaac 5760 taaatacaga attaatataa ctaacaaaca cctggtctga aataacaagg tgatctaccc 5820 tggaaggaac ccagctggtg ggccaggagc ggtggctcac acctgtaatt ccagcacttt 5880 gggaggctga gacaggagga tcactggagt ccaggagttt gagaccagcc tgggcaacat 5940 ggcaaaaccc agtgtgcttc tgttgtccca gctacactac tcaggaggct gaggcaggag 6000 tatgacttga gcctgggagg gggaggttgc agagaactga tattgcacca ccactgcact 6060 ccagcctggg tgacacagca aaaccctatc tcaaaaaaaa aaaaaaaaaa aaggaaccca 6120 gctggttcct gtaggtgtgc aataataaca accagaggaa gaaaaggaag acgatttccc 6180 agatgaagaa gggcagctgg accttcggac 6210 // Output file format The output is a standard EMBOSS report file. The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq. See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats. By default the output is in 'seqtable' format. Output files for usage example File: k00650.tfscan ######################################## # Program: tfscan # Rundate: Fri 15 Jul 2011 12:00:00 # Commandline: tfscan # -sequence tembl:k00650 # -menu v # Report_format: seqtable # Report_file: k00650.tfscan ######################################## #======================================= # # Sequence: K00650 from: 1 to: 6210 # HitCount: 9 #======================================= Start End Strand Accession Factor Sequence 3287 3292 + R04413 T00702; PU.1;Quality: 3; Species: mouse, Mus m usculus. ttcctc 5940 5944 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattu s norvegicus. tggca 3757 3761 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattu s norvegicus. tggca 2776 2780 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattu s norvegicus. tggca 2418 2422 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattu s norvegicus. tggca 2010 2014 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattu s norvegicus. tggca 1676 1680 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattu s norvegicus. tggca 1356 1360 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattu s norvegicus. tggca 2009 2014 + R00078 T00599; NF-1/L;Quality: 6; Species: rat, Rattu s norvegicus. ttggca #--------------------------------------- #--------------------------------------- #--------------------------------------- # Reported_sequences: 1 # Reported_hitcount: 9 #--------------------------------------- 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 marscan Finds matrix/scaffold recognition (MRS) signatures in DNA sequences 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 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 everyone and everything, from naive users to embedded scripts. Comments None