I have just installed FastA 3 on a WinXP computer. I would like to use the
program to query a local protein sequence database using an identity matrix.
The documentation says that I can do this using the command line switch:
-s idnaa.mat However, I can find this matrix among the files in the
download.
So my question: How do I get or construct this file? Is there a way to
construct other scoring matrices? Also, do I need to use the .mat extension
on the command line, or is that a default for a scoring matrix file?
Thanks for your help.
Steve Gendel
sgendel at cfsan.fda.gov
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