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aaindexextract |
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aaindexextract extracts amino acid property data from the AAINDEX database (see references 1, 2 and 3). One file for every amino acid property is created in the EMBOSS data directory data/AAINDEX. Each file corresponds to a single entry in the file aindex1 of the AAINDEX database.
The aaindexextract output files files may be used by any program that uses amino acid property data. For example, pepwindow and pepwindowall will take any one of these files if their -data qualifier is set to an appropriate file name. By default however these programs will use the standard EMBOSS data file Enakai.dat.
% aaindexextract Extract amino acid property data from AAINDEX AAINDEX database file: aaindex1.test |
Go to the input files for this example
Go to the output files for this example
Extract amino acid property data from AAINDEX
Version: EMBOSS:6.2.0
Standard (Mandatory) qualifiers:
[-infile] infile AAINDEX database file
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 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
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| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-infile] (Parameter 1) |
infile | AAINDEX database file | Input file | Required |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| (none) | ||||
| 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 |
H CHOP780101
D Normalized frequency of beta-turn (Chou-Fasman, 1978a)
R LIT:2004003a PMID:354496
A Chou, P.Y. and Fasman, G.D.
T Empirical predictions of protein conformation
J Ann. Rev. Biochem. 47, 251-276 (1978)
C PALJ810106 0.977 TANS770110 0.956 CHAM830101 0.946
CHOP780203 0.940 CHOP780216 0.929 CHOP780210 0.921
ROBB760113 0.907 GEIM800108 0.899 QIAN880133 0.897
QIAN880132 0.896 LEVM780103 0.893 PRAM900104 0.891
LEVM780106 0.890 ROBB760108 0.887 BEGF750103 0.885
ISOY800103 0.885 CRAJ730103 0.882 GEIM800111 0.878
PALJ810105 0.868 ROBB760110 0.863 NAGK730103 0.827
QIAN880131 0.824 AURR980114 -0.803 BEGF750101 -0.803
QIAN880107 -0.809 KANM800103 -0.824 AURR980109 -0.837
SUEM840101 -0.845
I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
0.66 0.95 1.56 1.46 1.19 0.98 0.74 1.56 0.95 0.47
0.59 1.01 0.60 0.60 1.52 1.43 0.96 0.96 1.14 0.50
//
H CHOP780201
D Normalized frequency of alpha-helix (Chou-Fasman, 1978b)
R PMID:364941
A Chou, P.Y. and Fasman, G.D.
T Prediction of the secondary structure of proteins from their amino
acid sequence
J Adv. Enzymol. 47, 45-148 (1978)
C PALJ810102 0.981 ROBB760101 0.969 ISOY800101 0.959
KANM800101 0.956 MAXF760101 0.956 TANS770101 0.947
BURA740101 0.917 GEIM800101 0.912 KANM800103 0.912
LEVM780104 0.886 NAGK730101 0.886 PALJ810101 0.881
QIAN880106 0.874 LEVM780101 0.873 PRAM900102 0.873
GEIM800104 0.868 RACS820108 0.868 AURR980108 0.867
AURR980109 0.859 AURR980112 0.856 CRAJ730101 0.851
QIAN880107 0.843 BEGF750101 0.841 QIAN880105 0.835
AURR980114 0.828 AURR980115 0.816 AURR980110 0.814
PALJ810109 0.814 AURR980111 0.813 ROBB760103 0.806
MUNV940101 -0.802 CRAJ730103 -0.808 ROBB760113 -0.811
MUNV940102 -0.812 CHAM830101 -0.828 NAGK730103 -0.837
I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
1.42 0.98 0.67 1.01 0.70 1.11 1.51 0.57 1.00 1.08
1.21 1.16 1.45 1.13 0.57 0.77 0.83 1.08 0.69 1.06
//
H CHOP780202
D Normalized frequency of beta-sheet (Chou-Fasman, 1978b)
R PMID:364941
A Chou, P.Y. and Fasman, G.D.
T Prediction of the secondary structure of proteins from their amino
acid sequence
J Adv. Enzymol. 47, 45-148 (1978)
[Part of this file has been deleted for brevity]
C ROBB760111 0.825
I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
0.058 0.085 0.091 0.081 0.128 0.098 0.064 0.152 0.054 0.056
0.070 0.095 0.055 0.065 0.068 0.106 0.079 0.167 0.125 0.053
//
H CHOP780216
D Normalized frequency of the 2nd and 3rd residues in turn (Chou-Fasman, 1978b)
R PMID:364941
A Chou, P.Y. and Fasman, G.D.
T Prediction of the secondary structure of proteins from their amino
acid sequence
J Adv. Enzymol. 47, 45-148 (1978)
C CHOP780203 0.979 GEIM800111 0.955 LEVM780106 0.953
LEVM780103 0.952 PRAM900104 0.951 CHAM830101 0.942
GEIM800108 0.942 QIAN880133 0.939 QIAN880132 0.931
TANS770110 0.930 CHOP780101 0.929 ISOY800103 0.921
PALJ810106 0.904 QIAN880134 0.900 CHOP780210 0.896
QIAN880135 0.884 PALJ810105 0.881 QIAN880131 0.873
NAGK730103 0.819 QIAN880120 -0.800 FAUJ880102 -0.807
KANM800103 -0.808 QIAN880107 -0.808 ROBB760103 -0.841
PTIO830101 -0.855 SUEM840101 -0.874
I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
0.64 1.05 1.56 1.61 0.92 0.84 0.80 1.63 0.77 0.29
0.36 1.13 0.51 0.62 2.04 1.52 0.98 0.48 1.08 0.43
//
H KYTJ820101
D Hydropathy index (Kyte-Doolittle, 1982)
R LIT:0807099 PMID:7108955
A Kyte, J. and Doolittle, R.F.
T A simple method for displaying the hydropathic character of a protein
J J. Mol. Biol. 157, 105-132 (1982)
C CHOC760103 0.964 JANJ780102 0.922 DESM900102 0.898
EISD860103 0.897 CHOC760104 0.889 WOLR810101 0.885
RADA880101 0.884 MANP780101 0.881 EISD840101 0.878
PONP800103 0.870 NAKH920108 0.868 JANJ790101 0.867
JANJ790102 0.866 PONP800102 0.861 MEIH800103 0.856
PONP800101 0.851 PONP800108 0.850 WARP780101 0.845
RADA880108 0.842 ROSG850102 0.841 DESM900101 0.837
BIOV880101 0.829 RADA880107 0.828 CIDH920104 0.824
KANM800104 0.824 LIFS790102 0.824 MIYS850101 0.821
RADA880104 0.819 NAKH900111 0.817 NISK800101 0.812
FAUJ830101 0.811 ARGP820103 0.806 ARGP820102 0.803
NAKH920105 0.803 KRIW790101 -0.805 CHOC760102 -0.838
MONM990101 -0.842 GUYH850101 -0.843 RACS770102 -0.844
JANJ780103 -0.845 ROSM880101 -0.845 PRAM900101 -0.850
JANJ780101 -0.852 GRAR740102 -0.859 MEIH800102 -0.871
ROSM880102 -0.878 OOBM770101 -0.899
I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
1.8 -4.5 -3.5 -3.5 2.5 -3.5 -3.5 -0.4 -3.2 4.5
3.8 -3.9 1.9 2.8 -1.6 -0.8 -0.7 -0.9 -1.3 4.2
//
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This directory contains output files, for example kytj820101.
H KYTJ820101
D Hydropathy index (Kyte-Doolittle, 1982)
R LIT:0807099 PMID:7108955
A Kyte, J. and Doolittle, R.F.
T A simple method for displaying the hydropathic character of a protein
J J. Mol. Biol. 157, 105-132 (1982)
C CHOC760103 0.964 JANJ780102 0.922 DESM900102 0.898
EISD860103 0.897 CHOC760104 0.889 WOLR810101 0.885
RADA880101 0.884 MANP780101 0.881 EISD840101 0.878
PONP800103 0.870 NAKH920108 0.868 JANJ790101 0.867
JANJ790102 0.866 PONP800102 0.861 MEIH800103 0.856
PONP800101 0.851 PONP800108 0.850 WARP780101 0.845
RADA880108 0.842 ROSG850102 0.841 DESM900101 0.837
BIOV880101 0.829 RADA880107 0.828 CIDH920104 0.824
KANM800104 0.824 LIFS790102 0.824 MIYS850101 0.821
RADA880104 0.819 NAKH900111 0.817 NISK800101 0.812
FAUJ830101 0.811 ARGP820103 0.806 ARGP820102 0.803
NAKH920105 0.803 KRIW790101 -0.805 CHOC760102 -0.838
MONM990101 -0.842 GUYH850101 -0.843 RACS770102 -0.844
JANJ780103 -0.845 ROSM880101 -0.845 PRAM900101 -0.850
JANJ780101 -0.852 GRAR740102 -0.859 MEIH800102 -0.871
ROSM880102 -0.878 OOBM770101 -0.899
I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
1.8 -4.5 -3.5 -3.5 2.5 -3.5 -3.5 -0.4 -3.2 4.5
3.8 -3.9 1.9 2.8 -1.6 -0.8 -0.7 -0.9 -1.3 4.2
//
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AAINDEX is a database of biochemical and physicochemical properties of amino acids and pairs of amino acids. aaindex1 for properties of each of the 20 single amino acids, aaindex2 for amino acid mutation matrices and aaindex3 for the amino-acid pair-wise contact potentials. All data are derived from the published literature. The file aaindex1 is required by aaindexextract and can be downloaded from the AAINDEX site: ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/aaindex1.
aaindexextract will write to the EMBOSS data directory data/AAINDEX. If you cannot find the output files then it is likely the data directory has been set to somewhere other than expected. To set explicitly the location of the EMBOSS data directory add the following to your emboss.default file:
ENV EMBOSS_DATA /path/to/the/EMBOSS/data/directory
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 codon usage tables from CUTG database |
| jaspextract | Extract data from JASPAR |
| 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 |
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.