Way to gap around a 100 bp insertion?

[pmiguel at bilbo.bio.purdue.edu]

>Is there some clever method to gap "around" a 100 bp insertion in genomic
>DNA? Lowering weights doesn't seem to help. 
>
>Thanks
>
>
>Paul Kowalski
>


  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:

	bestfit/len=0

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 
becomes unimportant.