FastA Help

Gendel, Steven M Steven.Gendel at CFSAN.FDA.GOV
Thu Oct 16 08:11:10 EST 2003

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


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


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