[ssml] 4 different results from BLAST using blosum62 & 50.

Kevin Karplus karplus at soe.ucsc.edu
Thu Aug 26 18:31:33 EDT 2004

The matrix is not the whole set of parameterization for BLAST.
There are also the gap costs and the lambda and K values used for
computing E-values.

Changing the matrix without correcting the other parameters leads to
uninterpretable results.

Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Senior member, IEEE	Board of Directors, ISCB (starting Jan 2005)
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.

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