[Biopython-dev] add dynamic programming alignment modules

Jeffrey Chang jchang at SMI.Stanford.EDU
Mon Aug 6 18:30:09 EDT 2001

At 11:02 AM -0400 8/4/01, Brad Chapman wrote:
>Hey Jeff;
>>  On the flight home from ISMB, I coded up some modules to do pairwise
>>  alignments.  I went ahead and put them into the Bio.Align package
>>  because they seem most appropriate there -- I hope nobody objects!
>Sweet! You are the man. And to think, I spent my whole time on the
>flight nursing a bad headache caused by staying up the entire night
>before (whoops, forgot to book a hotel room for that last night in
>Denmark!), and reading Hunter S. Thompson books.

Yeah, I don't know why you did that.  There were plenty of places you 
could have stayed!

>Seriously, I'm very happy to have this. I also have some dynamic
>programming stuff in my HMM module (which I am getting ready for
>potential submission right now -- working myself through the fun of
>writing up docs); once I get that ready we can see if there is
>anything there we can generalize and merge together.

Sounds good.  Although the boundary conditions are different, I 
believe the recurrences are the same, so we can share that part.  We 
only have to write it in C once!


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