I am looking for software (for any platform, but preferably Unix or
Macintosh), which will help me locate the endpoints of deletions in
plasmids. I have sequenced these endpoints, and I wish to find their
location in the original plasmid sequence.
I have tried this using various programs; staden (fasta, gap and
bestfit), and gcg. These only seem capable of finding the first
breakpoint, not the second. Am I doing something wrong, or is there a
specific program available that could help me in my quest?
Thanks for any and all help!