jaspextract |
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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.
% jaspextract Extract data from JASPAR JASPAR database directory [.]: jaspar |
Go to the output files for this example
Extract data from JASPAR Version: EMBOSS:6.4.0.0 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 |
This directory contains output files.
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.
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 |
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" 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" 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" 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" 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" 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" 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" 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" 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" 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" 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" |
This directory contains output files.
This directory contains output files.
This directory contains output files.
This directory contains output files.
This directory contains output files.
This directory contains output files.
This directory contains output files.
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 | 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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.