New Mutation Detection Features and Changes in 2003.0b1

Along with everything else, our mutation work was halted when our grant was cut, but several important changes relating to mutation detection are available in the 2003.0b1 release, and they are outlined here. Most of these new components are reasonably well tested, but none of the recent work has any user documentation.

1. mutscan is a new automatic mutation detection program which replaces both hetscan and tracediff. For our test data mutscan performed better that hetscan and tracediff, but a larger trial is needed to test its reliability. The version of pregap4 in the 2003.0b1 release is configured for mutscan.

2. The "Report Mutations" function in the "Commands" menu of the gap4 Contig Editor now has the option to automatically produce an html document which includes snapshots of the segments of traces which contain mutation tags (or differences). An example showing a cutdown report is available here

3. The gap4 contig editor has a new mode (set within the "Settings/Trace display" menu) which shows the traces embedded within the sequences. This makes it easier to compare many traces at once. The normal trace display still operates from this mode.


(Click for full size image)

4. hetins is a new program for automatically finding readings which contain heterozygous insertions and deletions. The current version is not as reliable as we would like and needs further work. The 2003.0b1 version of pregap4 is configured for hetins.