[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> </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). 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. :-) I didn't build a GUI, just a =
command line=20
interface. I'm using BLOSUM50 for the scoring matrix. =
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> </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. I'm not sure exactly how the Biojava working =
group=20
actually works. </FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Thanks for any feedback,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </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=
>
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