| ## 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.

### 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

Here is a sample session with backtranseq. Note that this is a human protein and so the default (human) codon frequency file is used (i.e. is not specified).

    % backtranseq
    Back translate a protein sequence
    Input sequence: sw:opsd_human
    Output sequence [opsd_human.fasta]:

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

    % backtranseq -cfile Edrosophila.cut
    Back translate a protein sequence
    Input sequence: sw:ach2_drome
    Output sequence [ach2_drome.fasta]:

## 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)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

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).

The output from the backtranslation of the human protein sw:opsd_human follows:

    % more opsd_human.fasta
    >OPSD_HUMAN P08100 RHODOPSIN.
    ATGAACGGCACCGAGGGCCCCAACTTCTACGTGCCCTTCAGCAACGCCACCGGCGTGGTG
    AGAAGCCCCTTCGAGTACCCCCAGTACTACCTGGCCGAGCCCTGGCAGTTCAGCATGCTG
    GCCGCCTACATGTTCCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTGACCCTGTAC
    GTGACCGTGCAGCACAAGAAGCTGAGAACCCCCCTGAACTACATCCTGCTGAACCTGGCC
    GTGGCCGACCTGTTCATGGTGCTGGGCGGCTTCACCAGCACCCTGTACACCAGCCTGCAC
    GGCTACTTCGTGTTCGGCCCCACCGGCTGCAACCTGGAGGGCTTCTTCGCCACCCTGGGC
    GGCGAGATCGCCCTGTGGAGCCTGGTGGTGCTGGCCATCGAGAGATACGTGGTGGTGTGC
    AAGCCCATGAGCAACTTCAGATTCGGCGAGAACCACGCCATCATGGGCGTGGCCTTCACC
    TGGGTGATGGCCCTGGCCTGCGCCGCCCCCCCCCTGGCCGGCTGGAGCAGATACATCCCC
    GAGGGCCTGCAGTGCAGCTGCGGCATCGACTACTACACCCTGAAGCCCGAGGTGAACAAC
    GAGAGCTTCGTGATCTACATGTTCGTGGTGCACTTCACCATCCCCATGATCATCATCTTC
    TTCTGCTACGGCCAGCTGGTGTTCACCGTGAAGGAGGCCGCCGCCCAGCAGCAGGAGAGC
    GCCACCACCCAGAAGGCCGAGAAGGAGGTGACCAGAATGGTGATCATCATGGTGATCGCC
    TTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCCTTCTACATCTTCACCCACCAGGGC
    AGCAACTTCGGCCCCATCTTCATGACCATCCCCGCCTTCTTCGCCAAGAGCGCCGCCATC
    TACAACCCCGTGATCTACATCATGATGAACAAGCAGTTCAGAAACTGCATGCTGACCACC
    ATCTGCTGCGGCAAGAACCCCCTGGGCGACGACGAGGCCAGCGCCACCGTGAGCAAGACC
    GAGACCAGCCAGGTGGCCCCCGCC

## 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

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.

## See also

Program name | Description
--- | ---
charge | Protein charge plot
checktrans | Reports STOP codons and ORF statistics of a protein sequence
coderet | Extract CDS, mRNA and translations from feature tables
compseq | Counts the composition of dimer/trimer/etc words in a sequence
emowse | Protein identification by mass spectrometry
freak | Residue/base frequency table or plot
iep | Calculates the isoelectric point of a protein
mwfilter | Filter noisy molwts from mass spec output
octanol | Displays protein hydropathy
pepinfo | Plots simple amino acid properties in parallel
pepstats | Protein statistics
pepwindow | Displays protein hydropathy
pepwindowall | Displays protein hydropathy of a set of sequences
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.

## Comments