[Biojava-l] Question about NiedlemanWunsch class

Andreas Prlic andreas at sdsc.edu
Tue Nov 4 22:30:16 UTC 2014

Hi Alexander,

Not sure, perhaps the javadoc is misleading (it comes from a high level
interface and the lower level implementations might do something slightly
different). Does the alignment image look correct? You might want to test
this with two shorter and perhaps quite similar sequences. Also, take a
look at the SmithWaterman approach, which does local alignments, rather
than global. Perhaps your two sequences are too far apart and the global
alignment does not yield good results...


On Mon Nov 03 2014 at 11:01:59 AM Александр Бескровный <
aleksandr.beskrovnyj at phystech.edu> wrote:

> Hello!
> 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!
> --
> Regards,
> Alexander Beskrovnyy
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