EMBOSS: backtranseq

Program backtranseq

Function

Back translate a protein sequence

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.

Usage

Here is a sample session with backtranseq.


% backtranseq
Input sequence: sw:opsd_human
Output sequence [opsd_human.fasta]:

Here is a session using a drosophila sequence and codon table:


% backtranseq -seq sw:ach2_drome -out stdout -cfile Edrosophila

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
  [-outfile]           seqout     Output sequence USA

   Optional qualifiers:
   -cfile              codon      Codon usage table name

   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default

[-sequence]
(Parameter 1) Sequence USA Readable sequence Required

[-outfile]
(Parameter 2) Output sequence USA Writeable sequence <sequence>.format

Optional qualifiers Allowed values Default

-cfile Codon usage table name Codon usage file in EMBOSS data path Ehum.cut

Advanced qualifiers Allowed values Default

(none)

Mandatory qualifiers	Allowed values	Default
[-sequence] (Parameter 1)	Sequence USA	Readable sequence	Required
[-outfile] (Parameter 2)	Output sequence USA	Writeable sequence	<sequence>.format
Optional qualifiers	Allowed values	Default
-cfile	Codon usage table name	Codon usage file in EMBOSS data path	Ehum.cut
Advanced qualifiers	Allowed values	Default
(none)

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.

To see the available EMBOSS codon usage files, run:


% embossdata -showall

To fetch one of the codon usage tables (for example 'Emus.cut') into your current directory for you to inspect or modify, run:


% embossdata -fetch -file Emus.cut

Notes

References

Warnings

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

Program name	Description
cusp	Create a codon usage table
getorf	Finds and extracts open reading frames (ORFs)
plotorf	Plot potential open reading frames
prettyseq	Output sequence with translated ranges
remap	Display a sequence with restriction cut sites, translation etc
showorf	Pretty output of DNA translations
showseq	Display a sequence with features, translation etc
transeq	Translate nucleic acid sequences

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Completed 6 Oct 1999

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.