[Biopython-dev] [Bug 1876] Bio.pairwise2 generates incorrect Needleman-Wunsch score_matrix

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1876





------- Comment #6 from bill at barnard-engineering.com  2005-10-07 18:38 -------
Since this (http://www.maths.tcd.ie/~lily/pres2/sld003.htm) algorithm is the
first entry found by googling "needleman wunsch", I should have read it more
carefully. It is now clear to me why the two score matrices are different. (In
this case they are tantalizingly similar...)

It might make a useful test for the module, to create alignment tuples with the
Durbin algorithm and compare those produced with the "McLysaght" algorithm.
I'll consider creating some tests like that, and contribute those.

I have not yet convinced myself the two algorithms are equivalent. Probably a
literature search in my local UC library would resolve that question. Do you
have a reference or web pointer to appropriate papers?

I would probably change this bug's status to "INVALID", which I presume is the
one for "Not a bug".




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