[Bioclusters] BLAT vs. BLAST and MegaBLAST

[bioclusters@bioinformatics.org]

jim_kent@pacbell.net
bioclusters@bioinformatics.org 
Dear Dr. Kent:
I am currently taking Dr. Bruce Moxon's UCSC Extension 
Bioinformatics Course: Design and Implementation of 
Bioinformatics Infrastructures.
As part of this course, I am writing a Term Paper 
focused on the analysis of effectiveness of BLAT as an 
alternative to BLAST & MegaBLAST, especially as 
regards the annotation of short, near exact 
matches,e.g., SNPs and their flanking sequences.
As you are the creator of BLAT, I wanted to touch base 
with you to get your guidance on this topic and 
perhaps get a chance to discuss related BLAT vs. BLAST 
questions with you.
For example, I would like to compare and contrast the 
BLAT vs. BLAST and MegaBLAST algorithms, fast 
alignment heuristics, scoring matrices, parmaters and 
implementations,output statistics and output parsing 
strategies.
Thanks for your time.
RSVP
Robin Turner,911 Laurel Ave.,Menlo Park, CA
robinturner@prodigy.net/650-321-7812