Hi Alexander
Maybe it would be helpful if you can post your code and also even the
sequences you are looking at, just copy/paste them into the email text.
Then it would be possible to have a look and see whether it is a bug or
a feature...
By the way, what version of Biojava are you using? is it 3.1? or are you
directly getting the latest snapshots from github?
Cheers
Jose
On 04/11/14 23:30, Andreas Prlic wrote:
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...
Andreas
On Mon Nov 03 2014 at 11:01:59 AM Александр Бескровный
<[email protected]
<mailto:[email protected]>> 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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