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Old 12-19-2014, 05:04 PM   #95
sdriscoll
I like code
 
Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 436
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Yeah that last point is totally fair. I'm also not totally sure that for most applications allowing a mismatch really tells me what I want to know anyways.

On another subject, are you familiar with the program Sailfish which uses kmer matching and the EM algorithm for gene expression? It is pretty much seal with an EM step that probabilistically estimates abundance.
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/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
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