BuildSA

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BuildSA

Index a protein database for fast searching.

Usage: java -Xmx3500M -cp MSGFPlus.jar edu.ucsd.msjava.msdbsearch.BuildSA 
	-d DatabaseFile (*.fasta or *.fa)
	[-tda 0/1/2] (0: target only, 1: target-decoy database only, 2: both)

Parameters:

BuildSA creates a suffix array of the protein database. For an input database file DBFileName.fasta, BuildSA will generate 4 auxiliary files (DbFileName.canno, DBFileName.cnlcp, DBFileName.csarr, DBFileName.cseq).It needs to be executed only once per each database file.