[BioC] homopolymer gap extension penalty in Biostrings

Frederick Ross fredross at uw.edu
Wed Mar 7 07:11:18 CET 2012

On 3/6/12 5:43 PM, Hervé Pagès wrote:
> Instead of trying to align seq1 to seq2, would it make sense to try
> to align runvals1 to runvals2 instead? Where runvals1 to runvals2 are
> defined as:

Actually, that's exactly what I'm doing at the moment. It works in the 
majority of cases, but there are, of course, corner cases where it will 
go wildly wrong.

> Anyway, I'm still not sure why "in the opposite strand" in
> specify a lower penalty for a gap extension when there is a
> homopolymeric insertion *in the opposite strand*
> Also, I'm still not clear about this:
> Another thing that would be useful would be per-strand gap creation
> and gap extension penalties.

I think this is a communication error. Noah is referring to homopolymer 
insertions versus heteropolymer insertions, nothing more, and we'd 
already moved in our thinking since Noah sent the message to using run 
length encoding (which is obviously simpler and better adapted).

Frederick Ross

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