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

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