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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:6.6.0.0
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
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 (c) 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
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