amino(1)
NAME
amino - displays the molecular structure of amino acids in
ASCII art :)
SYNOPSIS
amino [ -h ] [ -v | -s ] pattern ...
DESCRIPTION
amino is a program which displays ASCII art diagrams of
the molecular structure of the 20 amino acids present in
biological lifeforms. To see the diagram of a particular
amino amino acid, simply give the 3-letter, or 1-letter
abbreviation as an argument - or, alternatively, a DNA /
RNA codon.
The program works both on the command line, and as a CGI
script on a webserver - pick a nice day, copy it to the
cgi-bin directory of your webserver and try it! :)
EXAMPLES
- amino Leu
- will display the molecular structure for Leucine.
- amino list
- shows a list of all amino acids, with their abbrevia
tions. - amino codons
- shows a list of the DNA codons for all amino acids.
- amino polar
- shows the names of all amino acids with uncharged polar
side chains. - http://localhost/cgi-bin/amino
- will show the webinterface of this program, if it is
installed in the cgi-bin directory of your webserver :)
OPTIONS
- -h, --help
- Display a list of all command line options
- -d, --decode
- Read DNA codons from stdin and convert them to
3-letter amino acid codes. - -fd, --fastdecode
- Same as but faster, possibly more buggy...
- -e, --enhance
- Read single letters from the command line, and
expand them to the 3-letter abbreviations of the
amino acids. E.g. 'A' will expand to 'Ala' and '-'
will expand to 'Ter'. - -c, --condense
- Inverse of -enhance : (Ala -> A, Cys -> C, ...)
- -m x, --mode x
- Set output mode to x. Valid output modes are: text,
term, html and link_html.
BUGS
The codon table used in the program is the one supplied by
"Molecular Biology of The Cell" - I believe they are cor
rect for all eukaryotic lifeforms. However, for bacteria
and mitochondria the codons may be slightly different in
some places, so be warned!
HISTORY
- Written by Christian Steinruecken for the University of
Cambridge 2002