wobble

Function

Description

wobble draws a plot of the third base position variability in a nucleotide sequence as an indicator of potential coding regions. For each of the six possible translation frames, it plots a graph showing the percentage of G and C bases in the third position of codons in the frame within a window that is moved over the sequence. The mean of the third base percentage value is drawn as a horizontal line across the plots. Optionally, bases other than G and C can be chosen. Optionally, the same data can be written to an output file.

Usage

Command line arguments

Input file format

wobble reads a normal nucleic acid sequence USA.

Output file format

wobble plots a set of six graphs, one for each frame.

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

"Sequence too short for window" - The sequence must be longer than 3 times the window length.

"Specifying ACG&T is meaningless" - When you use the option -bases to specify the bases to look for, it is pointless to specify looking for all the possible bases as these should add to 100% all the time.

"No bases specified" - Similarly you have to specify some bases to look for otherwise you must plot a 0% line.

Exit status

It always exits with a status of 0, unless a fatal error is given.

Known bugs

None.

History

Target users

Comments