backtranseq
Function
Description
backtranseq takes a protein sequence and makes a best estimate of the
likely nucleic acid sequence it could have come from. It does this by
using a codon frequency table. For each amino acid, the corresponding
most frequently occuring codon is used in the construction of the nucleic
acid sequence.
Codon usage table name
backtranseq reads in a data file containing the codon frequency
tables. The default codon frequency table is 'Ehum.cut' - the human
codon frequency table. It is important to use a codon frequency table
that is appropriate for the species that your protein comes from.
See the Data Files section below for more details on these files.
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