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Protein scoring matrices in GCG 9

Tim Cutts tjrc1 at mole.bio.cam.ac.uk
Wed Mar 19 05:07:00 EST 1997


Hi people,

I have had a number of queries from users on my system about what
appears (to them) to be major differences between the output from pileup
in GCG 8 and GCG 9.

This seems to be due to the new default scoring matrix; does anyone
know what the rationale was behind this change, and why does it
produce such different answers to the previous GCG version?  This
seems to have confused a lot of users.  Of course I can tell them to
use -matrix=oldpep.cmp if they want the same results as GCG 8, but how
should they determine which is the appropriate scoring matrix to use?

Tim.



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