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aaindexextract |
AAINDEX is a database of properties of amino acids. See references [1] [2] [3].
The programs pepwindow and pepwindowall normally use the standard EMBOSS data file 'Enakai.dat' by default, but you can set their '-data' qualifier to use any of the files produced by aaextractindex from the AAINDEX database.
The AAINDEX database file 'aaindex1' can be downloaded from the AAINDEX site: ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1
% aaindexextract Extract data from AAINDEX Full pathname of file aaindex1: ~/aaindex1
Mandatory qualifiers:
[-inf] infile Full pathname of file aaindex1
Optional qualifiers: (none)
Advanced qualifiers: (none)
Associated qualifiers: (none)
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for required and optional values
-debug boolean Write debug output to program.dbg
-acdlog boolean Write ACD processing log to program.acdlog
-acdpretty boolean Rewrite ACD file as program.acdpretty
-acdtable boolean Write HTML table of options
-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 deaths
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| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-inf] (Parameter 1) |
Full pathname of file aaindex1 | Input file | Required |
| Optional qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced qualifiers | Allowed values | Default | |
| (none) | |||
H CHAM830102 D A parameter defined from the residuals obtained from the best correlation of the Chou-Fasman parameter of beta-sheet (Charton-Charton, 1983) R LIT:0907093b PMID:6876837 A Charton, M. and Charton, B. T The dependence of the Chou-Fasman parameters on amino acid side chain structure J J. Theor. Biol. 111, 447-450 (1983) * (Pro !) C I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V -0.118 0.124 0.289 0.048 0.083 -0.105 -0.245 0.104 0.138 0.230 -0.052 0.032 -0.258 0.015 0. 0.225 0.166 0.158 0.094 0.513 //
ENV EMBOSS_DATA /path/to/the/EMBOSS/data/directory
in the EMBOSS emboss.default file.
(Where '/path/to/the/EMBOSS/data/directory' is the location of your EMBOSS data as unpacked from the distribution file.)
| Program name | Description |
|---|---|
| cutgextract | Extract data from CUTG |
| printsextract | Extract data from PRINTS |
| prosextract | Builds the PROSITE motif database for patmatmotifs to search |
| rebaseextract | Extract data from REBASE |
| tfextract | Extract data from TRANSFAC |
The programs pepwindow and pepwindowall normally use the standard EMBOSS data file 'Enakai.dat' by default, but you can set their '-data' qualifier to use any of the files produced by aaextractindex.