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Hi Alexander<br>
<br>
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...<br>
<br>
By the way, what version of Biojava are you using? is it 3.1? or are
you directly getting the latest snapshots from github?<br>
<br>
Cheers<br>
<br>
Jose<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 04/11/14 23:30, Andreas Prlic wrote:<br>
</div>
<blockquote
cite="mid:CALthepwG+m-Bp6viqD4TmWARhRKBn0-7QFrVsc_gRQO112iV6g@mail.gmail.com"
type="cite">Hi Alexander,<br>
<br>
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...
<div><br>
</div>
<div>Andreas<br>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">On Mon Nov 03 2014 at 11:01:59 AM
Александр Бескровный <<a moz-do-not-send="true"
href="mailto:aleksandr.beskrovnyj@phystech.edu">aleksandr.beskrovnyj@phystech.edu</a>>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hello!<br>
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"<br>
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.<br>
I used SimpleGapPenalty and
SubstitutionMatrixHelper.getNuc4_4() as a parameters of
constructor of NiedlemanWunsch class. <br>
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.<br>
<br>
Thanks for your attention!<span lang="en"><span></span></span>
<div>
<div>
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<div>
<div><br>
-- <br>
<div>Regards, <br>
</div>
<div>Alexander Beskrovnyy<br>
</div>
</div>
</div>
</div>
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