Generation of Multiple PSSMs
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PFAM:
    	Multiple PSSMs are generated for every family, where the reference sequence 
for a family is chosen in a manner such that no two reference sequences per family
show greater than 40% sequence identity. Query anchored PSSMs are generated
using PSI-BLAST i.e. by searching the reference sequence in a family specific
sequence database.

PALI: 
	Multiple PSSMs are generated by considering members of known 3-D structure in a 
SCOP family as reference sequences such that no two sequences share more than
80% identity.

	The parameters such as e-value, sequence identity(%) and query coverage(%) are
adjusted such that the PSSMs are not biased towards the closely related homologues.