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 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><div><div><div><div><div><div><br>-- <br><div>Regards, <br></div><div>Alexander Beskrovnyy<br></div>
</div></div></div></div></div></div></div></div></div>
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