backtranambig
Function
Description
backtranambig takes a protein sequence and makes the nucleic
acid sequence it could have come from. It does this by generating
nucleotide ambiguity codes that represent all possible codons for each
amino acid.
The resulting ambiguous nucleotide sequence can be translated to the
original protein using transeq, which will recognise highly
redundant codons (for example "WSN" for serine) as being produced by a
program such as backtranambig.
Genetic code
backtranambig needs a genetic code to generate the ambiguous
codons. The default genetic code is the standard ('Universal') code.
Usage
Command line arguments
Input file format
Any DNA sequence USA.
Output file format
The output is a nucleotide sequence containing the most favoured back
translation of the specified protein, and using the specified
translation table (which defaults to human).
Data files
The codon usage table is read by default from "Ehum.cut" in the 'data/CODONS'
directory of the EMBOSS distribution. If the name of a codon usage file
is specified on the command line, then this file will first be searched
for in the current directory and then in the 'data/CODONS' directory of
the EMBOSS distribution.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
"Corrupt codon index file" - the codon usage file is incomplete or empty.
"The file 'drosoph.cut' does not exist" - the codon usage file cannot be opened.
Exit status
This program always exits with a status of 0, unless the codon usage
table cannot be opened.
Known bugs
None.
Author(s)
History
Target users
Comments