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 _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
