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