jaspextract

Function

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

Command line arguments

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.

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.

Author(s)

History

Target users

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