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
- 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 unless an error is reported
Known bugs
None.
Author(s)
History
Target users
Comments