#	cobbler config file for SWAT profile output
#		Make a PSSM for each block (BL, FR, QM)
#		Select consensus residue based on pairwise scores
#			from blosum55.iij (TY 2, SU)
#		Embed the PSSM in the closest sequence from test.blks,
#			which is assumed to be in test.pros with the
#			same name and position (DB test.pros)
#		Trim the embbed PSSM to within 10 aas before the first
#			block and after the last block (TR 10)
#		Print a profile using the PSSM inside the blocks and 
#			and single55.mat outside them (MA, PF)
#	MA line triggers profile output, PF line specifies profile format
#	swat.cob contains the embedded sequence
#	swat.cob.prf contains the embedded pssm
#
#	Execute swat:   swat swat.cob <database> -M swat.cob.prf
#
TY	2
SU	blosum55.iij
BL	test.blks
FR	default.amino.frq
QM	blosum55.qij
TR	10
DB	test.pros
MA	single55.mat
PF	SWAT
OU	swat.cob
