<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yui_3_16_0_1_1434305574862_160708">Hi biojava,</div><div id="yui_3_16_0_1_1434305574862_160710"><br></div><div id="yui_3_16_0_1_1434305574862_160712" 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 id="yui_3_16_0_1_1434305574862_160926" dir="ltr"><br></div><div id="yui_3_16_0_1_1434305574862_160924" dir="ltr">biojava<br></div><div id="yui_3_16_0_1_1434305574862_160825" dir="ltr">TTGGGGCCTCTAAACGGGGTCTT<br style="" class="">TTGGGGC-TCTAAC--GGGTCTT<br style="" class="">TTGGGGCCTCTAAACGGG-TCTT<br style="" class=""><br style="" class="">clustal<br style="" class="">TTGGGGCCTCTAAACGGGGTCTT<br style="" class="">TTGGGG-CTCT-AACGGG-TCTT<br style="" class="">TTGGGGCCTCTAAACGGG-TCTT<br style="" class="">****** **** ****<br></div><div id="yui_3_16_0_1_1434305574862_161005">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 id="yui_3_16_0_1_1434305574862_161067"><br></div><div id="yui_3_16_0_1_1434305574862_161069">Cheers</div><div id="yui_3_16_0_1_1434305574862_161071">Stefan</div><div id="yui_3_16_0_1_1434305574862_161073">p.s.<br></div><div id="yui_3_16_0_1_1434305574862_161075" 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 id="yui_3_16_0_1_1434305574862_161077" dir="ltr">Does any of you guys have a copy of the IUB scoring matrix? which would be my next try?</div><div id="yui_3_16_0_1_1434305574862_161079" dir="ltr"><br></div><div dir="ltr" style="" class="" id="yui_3_16_0_1_1434305574862_160667"> <br style="" class=""></div></div></body></html>