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EMBOSS: inforesidue
inforesidue

 

Wiki

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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:6.4.0.0

   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