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