[Biojava-l] Needleman-Wunsch implemented in Java

[Dave Keller]

This is creepy.  I was just going to post the same thing last night but 
was too tired.  :-)

I couldn't find this implementation in BioJava either.  I was going to 
ask the list yesterday about how to plug this into the framework using 
the dp and dp.twohead packages.  It's not clear in the documentation how 
to use PairDPCursor, DPMatrix, CellCalculator, etc. in order to 
accomplish a global alignment.  Is there an UML diagram that shows how 
this is accomplished or could someone explain how they felt the dp 
package would be used to do alignments?  Also, I would be curious to see 
how you implemented it in the framework.

What I wrote does everything using the Symbol and SymbolLists.  So, all 
I need to do is to put the dp interfaces on top of it but I need to know 
how one would go about doing a global alignment  using BioJava.


On a side note, and this is probably inappropriate but I am doing anyway 
because I've been unemployed for so long, does anyone have a need for a 
software engineer who wants to eventually become a bioinformatician or 
computational biologist?  I want to go back to school for my Masters in 
the fall of '03 but I would like to find a job for the next year doing 
some sort of biology software.  I have a BS in Computer Science as well 
as a Minor in Mathematics.   I have taken college level Chemistry and 
Physics and have been teaching myself molecular bio and genetics.  I 
currently reside in Boston but am willing and able to move.  Please let 
me know if anyone has any leads, I really need to find something soon 
and although beggers can't be choosers, I really would like to get some 
bioinformatics experience.  Thank you.


Dave