<div dir="ltr">Hi Stefan,<div><br></div><div>what substitution matrix did you use? Nuc-4_4 ? BioJava comes with a wide range of substitution matrices. The gap penalties depend heavily on the choice of matrix.</div><div><br></div><div><a href="https://github.com/biojava/biojava/tree/cb8da7bf718b76e35a408731c1f122b412adc884/biojava-alignment/src/main/resources">https://github.com/biojava/biojava/tree/cb8da7bf718b76e35a408731c1f122b412adc884/biojava-alignment/src/main/resources</a><br></div><div><br></div><div>The IUB scoring matrix might be actually one of the few matrices not supported yet, but should be easy to add if needed. Is it correct that all matches score 1.9; all mismatches score 0? </div><div><br></div><div>Andreas</div><div><br></div><div><br></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jun 16, 2015 at 6:07 PM, stefan harjes <span dir="ltr"><<a href="mailto:stefanharjes@yahoo.de" target="_blank">stefanharjes@yahoo.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><div style="color:rgb(0,0,0);font-family:HelveticaNeue,'Helvetica Neue',Helvetica,Arial,'Lucida Grande',sans-serif;font-size:16px;background-color:rgb(255,255,255)"><div>Hi biojava,</div><div><br></div><div dir="ltr">I am fighting with the multiple alignment of several DNASequences. When I use the biojava computation I get alignments errors regarding the gaps. Clustalx computes a much better result in comparison:</div><div dir="ltr"><br></div><div dir="ltr">biojava<br></div><div dir="ltr">TTGGGGCCTCTAAACGGGGTCTT<br>TTGGGGC-TCTAAC--GGGTCTT<br>TTGGGGCCTCTAAACGGG-TCTT<br><br>clustal<br>TTGGGGCCTCTAAACGGGGTCTT<br>TTGGGG-CTCT-AACGGG-TCTT<br>TTGGGGCCTCTAAACGGG-TCTT<br>****** **** ****<br></div><div>The most important difference is the second gap in the middle sequence, which is obviously better aligned in clustal. Any hints as to how to improve the biojava parameters/algorithms? <br></div><div><br></div><div>Cheers</div><span class=""><font color="#888888"><div>Stefan</div></font></span><div>p.s.<br></div><div dir="ltr">I already tried to implement the actual gapPenalty which clustal uses which is 10/.1 for the pairwise and 10/.2 for the multiple alignment. (i.e. I changed all java short types to int, scaled all scoring parameters including the matrix by 10 and implemented two different gapPenalties in the two alignments). Unfortunately this does not change anything. <br></div><div dir="ltr">Does any of you guys have a copy of the IUB scoring matrix? which would be my next try?</div><div dir="ltr"><br></div><div dir="ltr"> <br></div></div></div><br>_______________________________________________<br>
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