inforesidue |
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% 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
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 |
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 |
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:
Program name | Description |
---|---|
infobase | Return information on a given nucleotide base |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.