EMBOSS: aaindexextract

| aaindexextract

## Function

Extract amino acid property data from AAINDEX

## Description

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`.

## Usage

Here is a sample session with aaindexextract

    % 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

## Command line arguments

       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. 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
--- | --- | ---
[-infile] (Parameter 1) | AAINDEX database file | Input file | Required
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

The AAINDEX database file 'aaindex1' can be downloaded from the AAINDEX site: ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/

### Input files for usage example

### File: aaindex1.test

    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
    //

## Output file format

One file for every entry in the AAINDEX database is created in the EMBOSS standard 'data/AAINDEX' directory. For example, the file 'kytj820101':

### Output files for usage example

### Directory: AAINDEX

This directory contains output files, for example kytj820101.

### File: AAINDEX/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
    //

## Data files

None.

## Notes

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.

## References

1. Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2, 93-100 (1988). [UI:89221001]
2. Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36 (1996). [UI:96272030]
3. Kawashima, S., Ogata, H., and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 27, 368-369 (1999). [UI:99063742]

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
cutgextract | Extract codon usage tables from 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.

## Author(s)

Peter Rice (pmr © ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

## History

Written (25 June 2002) - Peter Rice

## Target users

This program is intended to be used by administrators responsible for software and database installation and maintenance.

## Comments

None