sixpack

Function

Description

sixpack takes a nucleic acid sequence and writes out the forward and reverse senses of the sequence with the 3 forward and three reverse translations in a pretty display format.

It also writes a file containing the open reading frames that are larger than the specified minimum size (default 1 base, showing all possible open reading frames). These open reading frames are written as protein sequences in the default output sequence format.

An open reading frame is defined in this program as any possible translation between two STOP codons.

Algorithm

The nucleic acid sequence is read in.
The required genetic code is read in from the EGC* data files.
The three forward and three reverse translations are created.
The name and description are written to the ouput display file.
Any required regions to be changed to upper case are changed.
Any required regions to be highlighted in HTML colour tags are changed.
The reverse sense sequence is placed below the forward sequence.
The forward translations are placed above the sequences.
The reverse translation are placed below the sequences.
The display is written out, split at the ends of lines.
Any ORFs that are longer than the specified minimum size are written to the output sequence file.

Usage

Command line arguments


Input file format

sixpack reads any normal sequence USAs.

Output file format

Data files

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Author(s)

History

Target users

Comments