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 3 JASPAR matrix sets 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 the uncompressed and extracted JASPAR_CORE.tgz, JASPAR_FAM.tgz and JASPAR_PHYLOFACTS.tgz files provided in the JASPAR MatrixDir download directory of the JASPAR homepage (http://jaspar.genereg.net).

The files will usually be extracted in the same directory thereby creating a directory containing subdirectories JASPAR_CORE, JASPAR_FAM and JASPAR_PHYLOFACTS. Given a directory specification, jasparextract will search for these subdirectories and process the files in any that exist. jasparextract will warn the user if any of the three subdirectories do not exist.

Output file format

The output file format is currently the same as the JASPAR distribution format.

Data files

None

Notes

The home page of REBASE 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

The program will warn you if any of the JASPAR_CORE, JASPAR_FAM or JASPAR_PHYLOFACTS subdirectories do not exist.

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

Comments