>Is there some clever method to gap "around" a 100 bp insertion in genomic
>DNA? Lowering weights doesn't seem to help.
I've found setting the length penalty to 0 allows me to compare cDNA with
genomic sequence fairly well with bestfit or gap. I just use the command
line parameter, ie:
So it should allow you to gap "around" a 100 bp insert. I'm not sure, but I
think mismatches are still penalized normally but the length of a gap