[Genome] Alignment techniques for finding SNPs (and other polymorphisms)

[David Garfield]

Hi genome-crew,

     I've got a question about the best ways of using alignment  
software to locate SNPs.  I'm working with the sea urchin genomes  
(the S. purpuratus 2.0 release along with the recently added 1.2x  
coverage 454 sequences of the related S. franciscanus and A. fragilis).

	I've had great luck using blastz/TBA to do whole genome alignments  
before, but in this case I'd like to make use of the high levels of  
polymorphism in urchin populations and track not only which regions  
of the A. frag and S. franc genomes map to the annotated S. purp  
sequence, but also track the polymorphisms that pop up on the  
occasions where the 454 sequences cover both halpotypes from the same  
region (and perhaps use the WGS reads from S_purp to find  
polymorphisms within that genome).


Any suggestions on how to proceed?  I'm savy enough, I think, to  
figure out how to use most of the programs out there, and can  
certainly parse outputs of one format to another, but given the  
bewildering array of alignment tools out there, I'd rather not  
reinvent the wheel if folks have already tried to do something similar.


Thanks in advance,

David Garfield
Wray Lab
Duke University