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

[Kayla Smith]

Hello David,

I've asked Jim Kent for advice on what your question.  He says that
the divergence level in the sea urchin is high enough you might want to 
stick with blastz.  But that on the other hand BLAT would be much faster 
and would probably only miss about 1%.

Our source code is available for download here:
http://genome.ucsc.edu/FAQ/FAQdownloads#download27

Good luck with your research.  If you have any questions about the 
Genome Browser, please don't hesitate to contact us again.

Kayla Smith
UCSC Genome Bioinformatics Group


David Garfield wrote:
> 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
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