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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) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
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 |
domainer | Reads protein coordinate files and writes domains coordinate files |
funky | Reads clean coordinate files and writes file of protein-heterogen contact data |
groups | Removes redundant hits from a scop families file |
hetparse | Converts raw dictionary of heterogen groups to a file in embl-like format |
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one |
pdbparse | Parses pdb files and writes cleaned-up protein coordinate files |
pdbtosp | Convert raw swissprot:pdb equivalence file to embl-like format |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
scope | Convert raw scop classification file to embl-like format |
scopnr | Removes redundant domains from a scop classification file |
scopparse | Converts raw scop classification files to a file in embl-like format |
scopseqs | Adds pdb and swissprot sequence records to a scop classification file |
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.