EMBOSS: jaspextract

| jaspextract

## Wiki

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## Function

Extract data from JASPAR

## Description

JASPAR is a collection of transcription factor DNA-binding preferences, modelled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences.

JASPAR is the only database with this scope where the data can be used with no restrictions (open-source).

This program copies the JASPAR distribution into its component matrix sets (e.g. JASPAR_CORE, JASPAR_PHYLOFACTS etc) and copies them into the EMBOSS data directories, performing any necessary conversions

The home page of JASPAR is: http://jaspar.genereg.net/

The EMBOSS program jaspscan will not work unless this program is run.

Running this program may be the job of your system manager.

## Usage

Here is a sample session with jaspextract

    % jaspextract
    Extract data from JASPAR
    JASPAR database directory [.]: jaspar

Go to the output files for this example

## Command line arguments

    Extract data from JASPAR
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-directory]         directory  The FlatFileDir directory containing the
                                      .pfm files and the matrix_list.txt file

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-directory" associated qualifiers
       -extension1         string     Default file extension

       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
[-directory] (Parameter 1) | directory | The FlatFileDir directory containing the .pfm files and the matrix_list.txt file | Directory |
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-directory" associated directory qualifiers
-extension1 -extension_directory | string | Default file extension | Any string |
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

The input files are part of the uncompressed and extracted Archive.zip file provided in the JASPAR html/DOWNLOAD directory of the JASPAR homepage (http://jaspar.genereg.net). After extracting the file you should specify the all_data/FlatFileDir directory when running jasparextract. It is advisable to first delete any old data files from your EMBOSS data file area e.g. from the /usr/local/emboss/share/EMBOSS/data/JASPAR_* directories

## Output file format

The output file format is currently the same as the JASPAR distribution format, but with the matrix files separated into directories according to their type.

### Output files for usage example

### Directory: JASPAR_CNE

This directory contains output files.

### Directory: JASPAR_CORE

This directory contains output files, for example MA0070.1.pfm MA0071.1.pfm MA0072.1.pfm MA0073.1.pfm MA0074.1.pfm MA0075.1.pfm MA0076.1.pfm MA0077.1.pfm MA0078.1.pfm MA0079.1.pfm and matrix_list.txt.

### File: JASPAR_CORE/MA0070.1.pfm

     5  3 16  1  0 17 17  0  0 16 12  8
     6  9  1  1 18  1  0  0 18  1  0  2
     2  3  1  0  0  0  0  1  0  0  1  2
     5  3  0 16  0  0  1 17  0  1  5  6

### File: JASPAR_CORE/MA0071.1.pfm

    15  9  6 11 21  0  0  0  0 25
     1  1 12  2  0  0  0  0 25  0
     2  0  4  5  4 25 25  0  0  0
     7 15  3  7  0  0  0 25  0  0

### File: JASPAR_CORE/MA0072.1.pfm

     9 17 15 35 23  2  0 28  0  0  0  0 36 15
     8  2  0  1  0 12  0  0  0  0  0 36  0  6
     8  7  3  0  0 13  0  8 36 36  0  0  0 10
    11 10 18  0 13  9 36  0  0  0 36  0  0  5

### File: JASPAR_CORE/MA0073.1.pfm

     3  1  3  0  7  9  8  4  0 11  4  1  3  4  2  4  4  4  1  4
     8 10  8 11  4  2  3  6 11  0  7 10  8  6  9  5  5  6  7  4
     0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  1  0  3  2
     0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  2  1  1  0  1

### File: JASPAR_CORE/MA0074.1.pfm

     3  0  0  0  0  9  4  2  2  5  0  0  1  0  7
     0  0  0  0  9  0  2  4  0  0  0  0  0  9  1
     7 10  9  0  0  1  0  2  8  5 10  0  0  0  2
     0  0  1 10  1  0  4  2  0  0  0 10  9  1  0

### File: JASPAR_CORE/MA0075.1.pfm

    52 59  0  0 58
     2  0  0  0  0
     4  0  1  0  1
     1  0 58 59  0

### File: JASPAR_CORE/MA0076.1.pfm

    16  0  0  0  0 20 16  4  1
     1 20 20  0  0  0  0  1  6
     2  0  0 20 20  0  0 15  0
     1  0  0  0  0  0  4  0 13

### File: JASPAR_CORE/MA0077.1.pfm

    24 54 59  0 65 71  4 24  9
     7  6  4 72  4  2  0  6  9
    31  7  0  2  0  1  1 38 55
    14  9 13  2  7  2 71  8  3

### File: JASPAR_CORE/MA0078.1.pfm

     7  8  3 30  0  0  0  0  0
     9  8 18  0  1  0  0  0 17
     6  4  1  0  0  0 31  2 10
     9 11  9  1 30 31  0 29  4

### File: JASPAR_CORE/MA0079.1.pfm

    1 2 0 0 0 2 0 0 1 2
    1 1 0 0 5 0 1 0 1 0
    4 4 8 8 2 4 5 6 6 0
    2 1 0 0 1 2 2 2 0 6

### File: JASPAR_CORE/matrix_list.txt

    MA0072.1	17.4248426117905	RORA_2	Zinc-coordinating	; acc "NP_599022" ; collection "CORE" ; comment "isoform type" ; family "Hormone-nuclear Receptor" ; medline "7926749" ; pazar_tf_id "TF0000048" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
    MA0075.1	9.06306510239134	Prrx2	Helix-Turn-Helix	; acc "Q06348" ; collection "CORE" ; comment "-" ; family "Homeo" ; medline "7901837" ; pazar_tf_id "TF0000051" ; species "10090" ; tax_group "vertebrates" ; type "SELEX"
    MA0071.1	13.1897301896459	RORA_1	Zinc-coordinating	; acc "NP_599023" ; collection "CORE" ; comment "isoform type" ; family "Hormone-nuclear Receptor" ; medline "7926749" ; pazar_tf_id "TF0000047" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
    MA0073.1	22.2782723704014	RREB1	Zinc-coordinating	; acc "Q92766" ; collection "CORE" ; comment "-" ; family "BetaBetaAlpha-zinc finger" ; medline "8816445" ; pazar_tf_id "TF0000049" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
    MA0070.1	14.6408952002356	PBX1	Helix-Turn-Helix	; acc "Q5T486" ; collection "CORE" ; comment "-" ; family "Homeo" ; medline "7910944" ; pazar_tf_id "TF0000046" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
    MA0074.1	20.4511671987138	RXRA::VDR	Zinc-coordinating	; acc "P19793,P11473" ; collection "CORE" ; comment "heterodimer between RXRA and VDR" ; family "Hormone-nuclear Receptor" ; medline "8674817" ; pazar_tf_id "TF0000050" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
    MA0078.1	10.5018372361999	Sox17	Other Alpha-Helix	; acc "Q61473" ; collection "CORE" ; comment "-" ; family "High Mobility Group" ; medline "8636240" ; pazar_tf_id "TF0000054" ; species "10090" ; tax_group "vertebrates" ; type "SELEX"
    MA0079.1	9.7185757452318	SP1	Zinc-coordinating	; acc "P08047" ; collection "CORE" ; comment "-" ; family "BetaBetaAlpha-zinc finger" ; medline "2192357" ; pazar_tf_id "TF0000055" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
    MA0079.2	11.1288626921664	SP1	Zinc-coordinating	; acc "P08047" ; collection "CORE" ; comment "Annotations from PAZAR SP1 + SP1_MOUSE + SP1_HUMAN + SP1_RAT in the pleiades genes project (TF0000105, TF0000121, TF0000137, TF0000146)." ; family "BetaBetaAlpha-zinc finger" ; medline "17916232" ; pazar_tf_id "TF0000055" ; species "9606,10090,10116" ; tax_group "vertebrates" ; type "COMPILED"
    MA0077.1	9.07881462267178	SOX9	Other Alpha-Helix	; acc "P48436" ; collection "CORE" ; comment "-" ; family "High Mobility Group" ; medline "9973626" ; pazar_tf_id "TF0000053" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
    MA0076.1	14.123230134165	ELK4	Winged Helix-Turn-Helix	; acc "P28324" ; collection "CORE" ; comment "-" ; family "Ets" ; medline "8524663" ; pazar_tf_id "TF0000052" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"

### Directory: JASPAR_FAM

This directory contains output files.

### Directory: JASPAR_PBM

This directory contains output files.

### Directory: JASPAR_PBM_HLH

This directory contains output files.

### Directory: JASPAR_PBM_HOMEO

This directory contains output files.

### Directory: JASPAR_PHYLOFACTS

This directory contains output files.

### Directory: JASPAR_POLII

This directory contains output files.

### Directory: JASPAR_SPLICE

This directory contains output files.

## Data files

None

## Notes

The home page of JASPAR is: http://jaspar.genereg.net Running this program may be the job of your system manager.

## 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 unless an error is reported

## Known bugs

None.

## See also

Program name | Description
--- | ---
aaindexextract | Extract amino acid property data from AAINDEX
cutgextract | Extract codon usage tables from CUTG database
printsextract | Extract data from PRINTS database for use by pscan
prosextract | Process the PROSITE motif database for use by patmatmotifs
rebaseextract | Process the REBASE database for use by restriction enzyme applications
tfextract | Process TRANSFAC transcription factor database for use by tfscan

## 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 administrators responsible for software and database installation and maintenance.

## Comments

None