EMBOSS: inforesidue

| inforesidue

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Return information on a given amino acid residue

## Description

inforesidue reports the defined properties for all known residues, or for any residues specified by the user.

## Usage

Here is a sample session with inforesidue

    % inforesidue
    Return information on a given amino acid residue
    Amino acid residue code [ABCDEFGHIJKLMNOPQRSTUVWXYZ]:
    Output file [outfile.inforesidue]:

Go to the output files for this example

## Command line arguments

    Return information on a given amino acid residue
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-code]              string     [ABCDEFGHIJKLMNOPQRSTUVWXYZ] Enter IUPAC
                                      amino acids codes, e.g. A, C, D, E etc. (Any
                                      string)
      [-outfile]           outfile    [*.inforesidue] Output file name

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -aadata             datafile   [Eamino.dat] Amino acid properties
       -mwdata             datafile   [Emolwt.dat] Molecular weight data for amino
                                      acids

       Associated qualifiers:

       "-outfile" associated qualifiers
       -odirectory2        string     Output directory

       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
[-code] (Parameter 1) | string | Enter IUPAC amino acids codes, e.g. A, C, D, E etc. | Any string | ABCDEFGHIJKLMNOPQRSTUVWXYZ
[-outfile] (Parameter 2) | outfile | Output file name | Output file | <*>.inforesidue
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-aadata | datafile | Amino acid properties | Data file | Eamino.dat
-mwdata | datafile | Molecular weight data for amino acids | Data file | Emolwt.dat
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile | string | Output directory | 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

## Input file format

inforesidue uses a string of residue codes.

## Output file format

inforesidue outputs a text table of residue properties.

### Output files for usage example

### File: outfile.inforesidue

    Code Short Mnemonic             Charge     MolWt Properties                     Ambiguity
    A    Ala   alanine                 0.0   71.0788 tiny,small,aliphatic,nonpolar  A
    B    Asx   aspartate/asparagine   -0.5  114.5962 small                          DN
    C    Cys   cysteine                0.0  103.1388 tiny,small,nonpolar            C
    D    Asp   aspartate              -1.0  115.0886 small,polar                    D
    E    Glu   glutamate              -1.0  129.1155 polar                          E
    F    Phe   phenylalanine           0.0  147.1766 aromatic,nonpolar              F
    G    Gly   glycine                 0.0   57.0519 tiny,small,nonpolar            G
    H    His   histidine              +0.5  137.1411 aromatic,polar                 H
    I    Ile   isoleucine              0.0  113.1594 aliphatic,nonpolar             I
    J    ---   leucine/isoleucine      0.0  113.1594 aliphatic,nonpolar             IL
    K    Lys   lysine                 +1.0  128.1741 polar                          K
    L    Leu   leucine                 0.0  113.1594 aliphatic,nonpolar             L
    M    Met   methionine              0.0  131.1926 nonpolar                       M
    N    Asn   asparagine              0.0  114.1038 small,polar                    N
    O    ---   pyrrolysine            +1.0  237.3018 polar                          O
    P    Pro   proline                 0.0   97.1167 small,nonpolar                 P
    Q    Gln   glutamine               0.0  128.1307 polar                          Q
    R    Arg   arginine               +1.0  156.1875 polar                          R
    S    Ser   serine                  0.0   87.0782 tiny,small,polar               S
    T    Thr   threonine               0.0  101.1051 tiny,small,polar               T
    U    ---   selenocysteine          0.0  150.0388 tiny,small,nonpolar            U
    V    Val   valine                  0.0   99.1326 small,aliphatic,nonpolar       V
    W    Trp   tryptophan              0.0  186.2132 aromatic,nonpolar              W
    X    Xaa   unknown                 0.0  118.8860 (none)                         ACDEFGHIKLMNPQRSTVWY
    Y    Tyr   tyrosine                0.0  163.1760 aromatic,nonpolar              Y
    Z    Glx   glutamate/glutamine    -0.5  128.6231 polar                          EQ

## Data files

inforesidue reads the Eresidues.iub file to define IUB standard codes for nucleotides and ambiguity codes, and files Eamino.dat and Emolwt.dat to read other amino acid residue chemical proerties and molecular weights.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
infobase | Return information on a given nucleotide base

## Author(s)

Jon Ison
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## History

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None