jaspscan

 

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Function

Scans DNA sequences for transcription factors

Description

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]: 

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:6.3.0

   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

   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 (Core)
F (Fam)
P (Phylofacts)
N (CNE)
O (POLII)
S (SPLICE)
B (PBM)
L (PBM_HLH)
H (PBM_HOMEO)
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 Report output file <*>.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 any normal sequence USAs.

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
//

Output file format

jaspscan outputs a report format file.

Output files for usage example

File: m23100.jaspscan

########################################
# Program: jaspscan
# Rundate: Fri 15 Jan 2010 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:

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:

The column information is described on the JASPAR home page http://jaspar.genereg.net/

Notes

None.

References

  1. DNA binding sites: representation and discovery Bioinformatics. 2000 Jan;16(1):16-23
  2. 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
tfscan Identify transcription factor binding sites in DNA sequences

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 © emboss.open-bio.org) not to the original author.

History

Completed 23rd July 2007

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None