EMBOSS: backtranambig

backtranambig

Function

Description

backtranambig reads a protein sequence and writes the nucleic acid sequence it could have come from. It does this by using nucleotide ambiguity codes that represent all possible codons for each amino acid.

Algorithm

backtranambig needs a genetic code to generate an ambiguous codon for each amino acid. The default genetic code is the standard ("Universal") code, although many others are available via the '-table' qualifier. The codon usage tables correspdonding to these codes must exist in the EMBOSS data directory. See the section on "Data Files" below for more information.

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

The ambiguous nucleotide sequence generated by backtranambig 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.

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.