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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
Standard (Mandatory) qualifiers:
[-code] string [ABCDEFGHIJKLMNOPQRSTUVWXYZ] Enter IUPAC
amino acids codes, e.g. A, C, D, E etc. (Any
string is accepted)
[-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. 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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-code] (Parameter 1) |
Enter IUPAC amino acids codes, e.g. A, C, D, E etc. | Any string is accepted | ABCDEFGHIJKLMNOPQRSTUVWXYZ |
| [-outfile] (Parameter 2) |
Output file name | Output file | <*>.inforesidue |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -aadata | Amino acid properties | Data file | Eamino.dat |
| -mwdata | Molecular weight data for amino acids | Data file | Emolwt.dat |
Code Short Mnemonic Charge MolWt Properties Ambiguity A Ala alanine 0.0 71.0786 tiny,small,aliphatic,nonpolar A B Asx aspartate/asparagine -0.5 114.5960 small DN C Cys cysteine 0.0 103.1386 tiny,small,nonpolar C D Asp aspartate -1.0 115.0884 small,polar D E Glu glutamate -1.0 129.1152 polar E F Phe phenylalanine 0.0 147.1762 aromatic,nonpolar F G Gly glycine 0.0 57.0518 tiny,small,nonpolar G H His histidine +0.5 137.1408 aromatic,polar H I Ile isoleucine 0.0 113.1590 aliphatic,nonpolar I J --- leucine/isoleucine 0.0 113.1590 aliphatic,nonpolar IL K Lys lysine +1.0 128.1736 polar K L Leu leucine 0.0 113.1590 aliphatic,nonpolar L M Met methionine 0.0 131.1926 nonpolar M N Asn asparagine 0.0 114.1036 small,polar N O --- pyrrolysine +1.0 109.1300 polar O P Pro proline 0.0 97.1164 small,nonpolar P Q Gln glutamine 0.0 128.1304 polar Q R Arg arginine +1.0 156.1870 polar R S Ser serine 0.0 87.0780 tiny,small,polar S T Thr threonine 0.0 101.1048 tiny,small,polar T U --- selenocysteine 0.0 150.0326 tiny,small,nonpolar U V Val valine 0.0 99.1322 small,aliphatic,nonpolar V W Trp tryptophan 0.0 186.2128 aromatic,nonpolar W X Xaa unknown 0.0 144.0000 (none) ACDEFGHIKLMNPQRSTVWY Y Tyr tyrosine 0.0 163.1756 aromatic,nonpolar Y Z Glx glutamate/glutamine -0.5 128.6228 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 |
|---|---|
| infoalign | Display basic information about a multiple sequence alignment |
| infobase | Return information on a given nucleotide base |
| infoseq | Display basic information about sequences |
| seealso | Finds programs with similar function to a specified program |
| showdb | Displays information on configured databases |
| textsearch | Search the textual description of sequence(s) |
| tfm | Displays full documentation for an application |
| whichdb | Search all sequence databases for an entry and retrieve it |
| wossname | Finds programs by keywords in their short description |