showorf

Function

Description

showorf writes an input nucleotide sequence and its protein translation to an output file in a clear format that is suitable for publication. The translation can be done in any frame or combination of frames using an (optionally) specified genetic code.

Usage

Command line arguments

Input file format

showorf reads a normal nucleic acid sequence USA.

Output file format

As a sequence with high GC content (from Pseudomonas aeruginosa) X13776 has several overlapping open reading frames.

The true ORFs are 1..109 (amiB partial) 135..1292 (amiC) 1289..1879 (amiR) 1925..end (amiS partial)

Data files

Showorf uses the codon frequency files to translate the sequence.

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 with the '-cfile' option, 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

None.

Exit status

It exits with a status of 0. It always exits with status 0.

Known bugs

None.

Author(s)

History

Target users

Comments