[Biojava-l] Needleman-Wunsch implemented in Java

Heather Trumbower htrumbower@attbi.com
Sun, 2 Jun 2002 22:11:33 -0700


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Greetings:

I recently implemented Needleman-Wunsch for global alignment of 2 =
protein sequences in Java (1.3.1).   The part I found a bit tricky (and =
therefore possibly valuable to share) was deducing the alignment from =
the backtrace, but I think I've got it working -- at least it works =
right on all of my test data. :-)  I didn't build a GUI, just a command =
line interface.  I'm using BLOSUM50 for the scoring matrix.   I also =
made the easy modifications to calculate Smith Waterman (the scoring =
matrix and the backtrace directions), but I didn't build the sequence =
alignment for Smith Waterman (yet).

I'm wondering whether this is something already in Biojava, or if it =
might be interesting to put it out for discussion/review.  I'm not sure =
exactly how the Biojava working group actually works. =20

Thanks for any feedback,

Heather Trumbower
htrumbower@attbi.com


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<DIV><FONT face=3DArial size=3D2>Greetings:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I recently implemented Needleman-Wunsch =
for global=20
alignment of 2 protein sequences in Java (1.3.1).&nbsp;&nbsp; The part I =
found a=20
bit tricky (and therefore possibly valuable to share) was deducing the =
alignment=20
from the backtrace, but I think I've got it working -- at least it works =
right=20
on all of my test data.&nbsp;:-) &nbsp;I didn't build a GUI, just a =
command line=20
interface.&nbsp; I'm using BLOSUM50 for the scoring matrix.&nbsp;&nbsp; =
I also=20
made the easy modifications to calculate Smith Waterman (the scoring =
matrix and=20
the backtrace directions), but I didn't build the sequence alignment for =
Smith=20
Waterman (yet).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I'm wondering whether this is something =
already in=20
Biojava, or if it might be interesting to put it out for=20
discussion/review.&nbsp; I'm not sure exactly how the Biojava working =
group=20
actually works.&nbsp; </FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thanks for any feedback,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Heather Trumbower</FONT></DIV>
<DIV><FONT face=3DArial size=3D2><A=20
href=3D"mailto:htrumbower@attbi.com">htrumbower@attbi.com</A></FONT></DIV=
>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV></BODY></HTML>

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