jaspextract |
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.
% jaspextract Extract data from JASPAR JASPAR database directory [.]: jaspar |
Go to the output files for this example
Standard (Mandatory) qualifiers: [-directory] directory The directory containing the unzipped and untarred JASPAR_CORE, JASPAR_FAM and JASPAR_PHYLOFACTS subdirectories Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: (none) 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. 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 |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-directory] (Parameter 1) |
The directory containing the unzipped and untarred JASPAR_CORE, JASPAR_FAM and JASPAR_PHYLOFACTS subdirectories | Directory | |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
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.
This directory contains output files, for example MA0070.pfm MA0071.pfm MA0072.pfm MA0073.pfm MA0074.pfm MA0075.pfm MA0076.pfm MA0077.pfm MA0078.pfm MA0079.pfm and matrix_list.txt.
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 |
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 |
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 |
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 |
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 |
52 59 0 0 58 2 0 0 0 0 4 0 1 0 1 1 0 58 59 0 |
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 |
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 |
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 |
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 |
MA0073 22.2782723704014 RREB1 ZN-FINGER, C2H2 ; acc "Q92766" ; medline "8816445" ; seqdb "SWISSPROT" ; species "Homo sapiens" ; sysgroup "vertebrate" ; total_ic "22.2800" ; type "SELEX" MA0075 9.06306510239135 Prrx2 HOMEO ; acc "Q06348" ; medline "7901837" ; seqdb "SWISSPROT" ; species "Mus musculus" ; sysgroup "vertebrate" ; total_ic "9.0620" ; type "SELEX" MA0070 14.6408952002356 Pbx HOMEO ; acc "P40424" ; medline "7910944" ; seqdb "SWISSPROT" ; species "Homo sapiens" ; sysgroup "vertebrate" ; total_ic "14.6440" ; type "SELEX" MA0079 9.7185757452318 SP1 ZN-FINGER, C2H2 ; acc "P08047" ; medline "2192357" ; seqdb "SWISSPROT" ; species "Homo sapiens" ; sysgroup "vertebrate" ; total_ic "9.7160" ; type "SELEX" MA0077 9.07881462267179 SOX9 HMG ; acc "P48436" ; medline "9973626" ; seqdb "SWISSPROT" ; species "Homo sapiens" ; sysgroup "vertebrate" ; total_ic "9.0810" ; type "SELEX" MA0078 10.5018372361999 Sox17 HMG ; acc "Q61473" ; medline "8636240" ; seqdb "SWISSPROT" ; species "Mus musculus" ; sysgroup "vertebrate" ; total_ic "10.5030" ; type "SELEX" MA0071 13.1897301896459 RORA NUCLEAR RECEPTOR ; acc "P35397" ; medline "7926749" ; seqdb "SWISSPROT" ; species "Homo sapiens" ; sysgroup "vertebrate" ; total_ic "13.1920" ; type "SELEX" MA0072 17.4248426117905 RORA1 NUCLEAR RECEPTOR ; acc "P35398" ; medline "7926749" ; seqdb "SWISSPROT" ; species "Homo sapiens" ; sysgroup "vertebrate" ; total_ic "17.4230" ; type "SELEX" MA0074 20.4511671987138 RXR-VDR NUCLEAR RECEPTOR ; acc "P11473" ; medline "8674817" ; seqdb "SWISSPROT" ; species "Homo sapiens" ; sysgroup "vertebrate" ; total_ic "20.4520" ; type "SELEX" MA0076 14.123230134165 ELK4 ETS ; acc "P28324" ; medline "8524663" ; seqdb "SWISSPROT" ; species "Homo sapiens" ; sysgroup "vertebrate" ; total_ic "14.1230" ; type "SELEX" |
This directory contains output files.
This directory contains output files.
Running this program may be the job of your system manager.
Program name | Description |
---|---|
aaindexextract | Extract amino acid property data from AAINDEX |
cutgextract | Extract codon usage tables from from CUTG database |
printsextract | Extract data from PRINTS database for use by pscan |
prosextract | Processes 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 |