|
|
tfscan |
Please help by correcting and extending the Wiki pages.
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.
% 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
Identify transcription factor binding sites in DNA sequences
Version: EMBOSS:6.6.0.0
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
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-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
|
| Qualifier | Type | Description | Allowed values | Default | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||||||
| [-sequence] (Parameter 1) |
seqall | Nucleotide sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | ||||||||||||
| -menu | list | Select class |
|
V | ||||||||||||
| -custom | datafile | Transfac database data file (optional) | Data file | File in the data file path | ||||||||||||
| -mismatch | integer | Number of mismatches | Integer 0 or more | 0 | ||||||||||||
| [-outfile] (Parameter 2) |
report | Output report file name | (default -rformat seqtable) | <*>.tfscan | ||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||
| -minlength | integer | Display matches equal to or above this length | Integer 1 or more | 1 | ||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||
| (none) | ||||||||||||||||
| Associated qualifiers | ||||||||||||||||
| "-sequence" associated seqall qualifiers | ||||||||||||||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||||||||
| -send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 | ||||||||||||
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||||||||
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||||||||
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||||||||
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||||||||
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||||||||
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||||||||
| -scircular1 -scircular_sequence |
boolean | Sequence is circular | Boolean value Yes/No | N | ||||||||||||
| -squick1 -squick_sequence |
boolean | Read id and sequence only | Boolean value Yes/No | N | ||||||||||||
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||||||||
| -iquery1 -iquery_sequence |
string | Input query fields or ID list | Any string | |||||||||||||
| -ioffset1 -ioffset_sequence |
integer | Input start position offset | Any integer value | 0 | ||||||||||||
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |||||||||||||
| -sid1 -sid_sequence |
string | Entryname | Any string | |||||||||||||
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |||||||||||||
| -fformat1 -fformat_sequence |
string | Features format | Any string | |||||||||||||
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |||||||||||||
| "-outfile" associated report qualifiers | ||||||||||||||||
| -rformat2 -rformat_outfile |
string | Report format | Any string | seqtable | ||||||||||||
| -rname2 -rname_outfile |
string | Base file name | Any string | |||||||||||||
| -rextension2 -rextension_outfile |
string | File name extension | Any string | |||||||||||||
| -rdirectory2 -rdirectory_outfile |
string | Output directory | Any string | |||||||||||||
| -raccshow2 -raccshow_outfile |
boolean | Show accession number in the report | Boolean value Yes/No | N | ||||||||||||
| -rdesshow2 -rdesshow_outfile |
boolean | Show description in the report | Boolean value Yes/No | N | ||||||||||||
| -rscoreshow2 -rscoreshow_outfile |
boolean | Show the score in the report | Boolean value Yes/No | Y | ||||||||||||
| -rstrandshow2 -rstrandshow_outfile |
boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y | ||||||||||||
| -rusashow2 -rusashow_outfile |
boolean | Show the full USA in the report | Boolean value Yes/No | N | ||||||||||||
| -rmaxall2 -rmaxall_outfile |
integer | Maximum total hits to report | Any integer value | 0 | ||||||||||||
| -rmaxseq2 -rmaxseq_outfile |
integer | Maximum hits to report for one sequence | Any integer value | 0 | ||||||||||||
| 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 | ||||||||||||
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.
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 Ensembl-Gn; ENSG00000170345; Homo_sapiens.
DR Ensembl-Tr; ENST00000303562; Homo_sapiens.
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
[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
//
|
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.
######################################## # Program: tfscan # Rundate: Mon 15 Jul 2013 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 musculus. ttcctc 5940 5944 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattus norvegicus. tggca 3757 3761 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattus norvegicus. tggca 2776 2780 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattus norvegicus. tggca 2418 2422 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattus norvegicus. tggca 2010 2014 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattus norvegicus. tggca 1676 1680 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattus norvegicus. tggca 1356 1360 + R00079 T00599; NF-1/L;Quality: 6; Species: rat, Rattus norvegicus. tggca 2009 2014 + R00078 T00599; NF-1/L;Quality: 6; Species: rat, Rattus 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.
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:
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.
An old public domain version of TRANSFAC is available at: ftp://ftp.ebi.ac.uk/pub/databases/transfac/transfac32.tar.Z
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.
| Program name | Description |
|---|---|
| jaspscan | Scan DNA sequences for transcription factors |
| marscan | Find 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.
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.