Tehdyt toimenpiteet
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jaspscan |
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Function
Scans DNA sequences for transcription factorsDescription
jaspscan scans one or more DNA sequences for transcription factor binding sites from the JASPAR database. 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.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 jaspscan
% jaspscan -both
Scans DNA sequences for transcription factors
Input nucleotide sequence(s): tembl:m23100
Jaspar matrix set
C : Core
F : Fam
P : Phylofacts
N : CNE
O : POLII
S : SPLICE
B : PBM
L : PBM_HLH
H : PBM_HOMEO
Matrix set [C]:
Comma separated matrix list [all]: ma0079.1
Threshold percentage [80.0]:
Output report [m23100.jaspscan]:
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Go to the input files for this example
Go to the output files for this example
Command line arguments
Scans DNA sequences for transcription factors
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
-menu menu [C] Matrix set (Values: C (Core); F (Fam); P
(Phylofacts); N (CNE); O (POLII); S
(SPLICE); B (PBM); L (PBM_HLH); H
(PBM_HOMEO))
-matrices string [all] The name 'all' reads in all matrix
files from the selected
JASPAR matrix set. You can specify
individual matrices by giving
their names with commas between then, such
as:
'ma0001.1,ma0015*'.
The case of the names is not important. You
can specify a file of
matrix names to read in by giving the name
of the file holding the
matrix names with a '@' character in front
of it, for example,
'@matrix.list'.
Blank lines and lines starting with a hash
character or '!' are ignored and all other
lines are concatenated together with a comma
character ',' and then treated as the list
of enzymes to search
for.
An example of a file of matrix names is:
! my matrices
ma0001.1, ma0002.1
! other matrices
ma0010.1
ma0032*
ma0053.1 (Any string)
-threshold float [80.0] If the matrix score is greater than
or equal to this percentage
then a hit will be reported (Any numeric
value)
[-outfile] report [*.jaspscan] Output report file name
(default -rformat seqtable)
Additional (Optional) qualifiers:
-exclude string The names of any matrices to exclude from
the 'matrices'
list. Matrices are specified in the same way
as for the
selection list. (Any string)
-both boolean [N] If set then both the forward and reverse
strands are searched
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
|
| 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 | Matrix set |
|
C | ||||||||||||||||||
| -matrices | string | The name 'all' reads in all matrix files from the selected JASPAR matrix set. You can specify individual matrices by giving their names with commas between then, such as: 'ma0001.1,ma0015*'. The case of the names is not important. You can specify a file of matrix names to read in by giving the name of the file holding the matrix names with a '@' character in front of it, for example, '@matrix.list'. Blank lines and lines starting with a hash character or '!' are ignored and all other lines are concatenated together with a comma character ',' and then treated as the list of enzymes to search for. An example of a file of matrix names is: ! my matrices ma0001.1, ma0002.1 ! other matrices ma0010.1 ma0032* ma0053.1 | Any string | all | ||||||||||||||||||
| -threshold | float | If the matrix score is greater than or equal to this percentage then a hit will be reported | Any numeric value | 80.0 | ||||||||||||||||||
| [-outfile] (Parameter 2) |
report | Output report file name | (default -rformat seqtable) | <*>.jaspscan | ||||||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||||||
| -exclude | string | The names of any matrices to exclude from the 'matrices' list. Matrices are specified in the same way as for the selection list. | Any string | |||||||||||||||||||
| -both | boolean | If set then both the forward and reverse strands are searched | Boolean value Yes/No | No | ||||||||||||||||||
| 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 | ||||||||||||||||||
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||||||||||||||
| -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 | ||||||||||||||||||
Input file format
jaspscan 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:m23100' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:m23100
ID M23100; SV 1; linear; genomic DNA; STD; HUM; 2085 BP.
XX
AC M23100; M32822;
XX
DT 06-JUL-1989 (Rel. 20, Created)
DT 14-NOV-2006 (Rel. 89, Last updated, Version 10)
XX
DE Human insulin receptor (INSR) gene, exon 1, clones lambda-hINSR-(1-13).
XX
KW Alu repeat; insulin receptor.
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 1-1933
RX DOI; 10.1073/pnas.86.1.114.
RX PUBMED; 2911561.
RA Seino S., Seino M., Nishi S., Bell G.I.;
RT "Structure of the human insulin receptor gene and characterization of its
RT promoter";
RL Proc. Natl. Acad. Sci. U.S.A. 86(1):114-118(1989).
XX
RN [2]
RP 1-2085
RX PUBMED; 2210055.
RA Seino S., Seino M., Bell G.I.;
RT "Human insulin-receptor gene. Partial sequence and amplification of exons
RT by polymerase chain reaction";
RL Diabetes 39(1):123-128(1990).
XX
CC Draft entry and computer-readable sequence for [1] kindly submitted
CC by G.Bell, 14-MAR-1990.
XX
FH Key Location/Qualifiers
FH
FT source 1..2085
FT /organism="Homo sapiens"
FT /map="19p13.3-p13.2"
FT /mol_type="genomic DNA"
FT /dev_stage="foetus"
FT /tissue_type="liver"
FT /db_xref="taxon:9606"
FT repeat_region <1..76
FT /rpt_family="Alu"
FT exon 1541..1923
FT /gene="INSR"
FT /number=1
[Part of this file has been deleted for brevity]
FT /number=1
FT /note="alternative exon 1; G00-119-352"
FT exon 1548..1923
FT /gene="INSR"
FT /number=1
FT /note="alternative exon 1; G00-119-352"
FT sig_peptide 1824..1904
FT /gene="INSR"
FT /note="G00-119-352"
FT intron 1924..>2085
FT /gene="INSR"
FT /number=1
FT /note="G00-119-352"
XX
SQ Sequence 2085 BP; 417 A; 631 C; 702 G; 335 T; 0 other;
agatctggcc attgcactcc agcctgggca acagagaaaa actccatcta aaaaaaaaaa 60
aaaaaaaaaa aaaaaacaga gagagagaga gagagagaga gaaggaaacg gaactggggg 120
gaggatttgc aaaaatatgg ttagggatgg cacttcagag atgaagccat cctggagtgt 180
tacgggcaag ggaaatgctg gggcaaagcc ccagaggcag gaataggttt ggcctgttgc 240
atgaacagtg ggtccagctc ctagcaaact gtttattgaa tgaaagaaga atgaatgcct 300
tgggtctagg gttgtgctgg gcgctttctt aagttttctt tcccgggtac ctccccagaa 360
ctggcatgca ggtattatta aacccattac acaagtgaaa ctggcccaga gacagaaaag 420
tccctggtcc aagaccacac aggagtgagg ggtggaggaa ccctcctccc attgagttct 480
ggctttccta tactgaaagc cccttcctct cctgcagtaa ggtaggtgga accgctgtcc 540
cgccttgttg gtgaatgtcg ttgctagact tcagacacat acaggctggt ctgctgaaaa 600
tcagagatgt ccacctgcgc cctattcgag gtctccggcg tcttctttgg cgtcgtcttt 660
gccctttcag aagcgtctgc acatttttcc aggtgtcatt tctccaactt gaacacaggg 720
agcgcactgg gcacgcgggc acgtggctgt ccccaggggc ctggcttggg tctcgcccct 780
gggccggggc gcacgcgcgg gcgggacatc tgggggcgcc cacgcgctct gggacgagtg 840
tcgctggcca ggcccggact gaggaaaggc gagtgagaca ctactcgcct ggggtgcaaa 900
atttaaggga gtgaaaaaaa aaaaaaaaga aagaaaccaa aaccacctcg agtcaccaaa 960
ataaacattt taatgcagta ttttttaaaa aatcaacagg aatcctccaa agcccactat 1020
gaacaaaata gcaaaatggt agagaaagga tctgtgccgc tgcgtcgggc ctgtggggcg 1080
cctccggggg tctgaaactg gaggagactc ggggctgtag ggcgcgcgga tctggggcgc 1140
gccctcggtc ccggcgcgcc cagggcctcc cgcgcggggc ccggcacagg gaggcgggga 1200
ggcgggcggg gcggggcggg accgggcggc acctccctcc cctgcaagct ttccctccct 1260
ctcctgggcc tctcccgggc gcagagtccc ttcctaggcc agatccgcgc cgccttttcc 1320
cgcggcccgc acggggccca gctgacgggc cgcgttgttt acgggccgga gcagccctct 1380
ctcccgccgc ccgcccgcca cccgccagcc caggtgcccg cccgccagtc agctagtccg 1440
tcggtccgcg cgtccctctg tcccggagcc cgcagatcgc gacccagagc gcgcggggcc 1500
gagagccgag agacagtccc gggcgcagcg cggagctccg ggccccgaga tcctgggacg 1560
gggcccgggc cgcagcggcc ggggggtcgg ggccaccacc gcaagggcct ccgctcagta 1620
tttgtagctg gcgaagccgc gcgcgccctt cccggggctg cctctgggcc ctccccggca 1680
ggggggctgc ggcccgcggg tcgcgggcgt ggaagagaag gacgcgcggc ccccagcgcc 1740
tcttgggtgg ccgcctcgga gcatgacccc cgcgggccag cgccgcgcgc tctgatccga 1800
ggagaccccg cgctcccgca gccatgggca ccgggggccg gcggggagcg gcggccgcgc 1860
cgctgctggt ggcggtggcc gcgctgctac tgggcgccgc gggccacctg taccccggag 1920
agggtgagtc tgggggcgcg ggcgtgggcg gggagcgccg cgatggggag aggaccccac 1980
ccaagccaaa atcgatcccc cgcttgtgga ctgagaaccc tccccagggg cggggggcgg 2040
tggccaggac ggtagctcct gcatcgcgta gggggagcgg gaagc 2085
//
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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 report is in 'seqtable' format.
Output files for usage example
File: m23100.jaspscan
########################################
# Program: jaspscan
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: jaspscan
# -both
# -sequence tembl:m23100
# -matrices ma0079.1
# Report_format: seqtable
# Report_file: m23100.jaspscan
########################################
#=======================================
#
# Sequence: M23100 from: 1 to: 2085
# HitCount: 18
#
# Database scanned: JASPAR_CORE Threshold: 80.000
#
#=======================================
Start End Strand Score_Percent ID Name Species Class Supergroup Family Pazar_TF_ID Protein_Seq Experiment Source_PMID Info_Content Closest_Jaspar Closest_Transfac MCS_Score Built_From Sequence
117 126 + 82.143 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . gggggaggat
1191 1200 + 89.286 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . gaggcgggga
1203 1212 + 83.929 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . cgggcggggc
1208 1217 + 89.286 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . ggggcggggc
1213 1222 + 80.357 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . ggggcgggac
1704 1713 + 82.143 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . cgggcgtgga
1838 1847 + 82.143 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . ccggcgggga
1933 1942 + 82.143 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . ggggcgcggg
1945 1954 + 89.286 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . tgggcgggga
2027 2036 + 89.286 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . ggggcggggg
2032 2041 + 87.500 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . ggggggcggt
2034 2043 + 82.143 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . ggggcggtgg
1252 1261 - 80.357 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . gagggaggga
1304 1313 - 80.357 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . gcggcgcgga
1805 1814 - 80.357 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . agcgcggggt
1974 1983 - 89.286 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . tgggtggggt
2016 2025 - 80.357 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . ggggagggtt
2017 2026 - 87.500 MA0079.1 SP1 9606 Zinc-coordinating . . . P08047 SELEX 2192357 9.719 . . . . tggggagggt
#---------------------------------------
#---------------------------------------
|
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
The EMBOSS JASPAR transcription site files are stored in directory 'data/JASPAR/*' under the EMBOSS installation directory.
These files must first be set up using the program 'jaspextract'. Running 'jaspextract' may be the job of your system manager.
The data files are stored in the JASPAR directory of the standard EMBOSS data directory. The subdirectory names are:
- JASPAR_CORE Core files
- JASPAR_FAM Family files
- JASPAR_PHYLOFACT Phylogeny files
Notes
None.References
- DNA binding sites: representation and discovery Bioinformatics. 2000 Jan;16(1):16-23
- Applied bioinformatics for the identification of regulatory elements Nat Rev Genet. 2004 Apr;5(4):276-87
Warnings
None.Diagnostic Error Messages
None.Exit status
It always exits with status 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| marscan | Finds matrix/scaffold recognition (MRS) signatures in DNA sequences |
| tfscan | Identify transcription factor binding sites in DNA sequences |
Author(s)
Alan BleasbyEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.