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

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