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:6.4.0.0 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 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