[Biojava-l] Question about NiedlemanWunsch class

Александр Бескровный aleksandr.beskrovnyj at phystech.edu
Mon Nov 3 18:59:20 UTC 2014

I have a problem with aligning the sequences with the help of
NiedlemanWunsch class. The problem is following: I found the sequences,
where method "getSimilarity" got negative numbers, but the description
said: "It returns score as a similarity between 0.0 and 1.0"
I looked at the output of methods "getMaxScore", "getMinScore" and
"getScore", which are involved in calculations of method "getSimilarity",
and I have noticed, that "getMinScore" and "getMaxScore" got strange
numbers (maxScore was less than minScore or both were negative), but output
of "getScore" seemed adequate.
I used SimpleGapPenalty and SubstitutionMatrixHelper.getNuc4_4() as a
parameters of constructor of NiedlemanWunsch class.
According to rules, i can't attach file with sequences to my letter. But in
case it is possible, I would kindly ask you to explain me, how to do it
correctly,and then i'll send you the sequences. They are too long to be
send like a text in a letter.

Thanks for your attention!

Alexander Beskrovnyy
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