The files in this directory were produced as follows:

1plc.fa, 1auz.fa:
	FASTA sequences taken from http://www.rcsb.org

0042368.mod, 0035218.mod:
	SUPERFAMILY HMMs taken from http://supfam.org

0042368-1plc.a2m:
	hmmscore 0042368-1plc -i 0042368.mod -db 1plc.fa \
		-sw 2 -dpstyle 0 -adpstyle 5 -select_align 8

0035218-1auz.a2m:
	hmmscore 0035218-1auz -i 0035218.mod -db 1auz.fa \
		-sw 2 -dpstyle 0 -adpstyle 5 -select_align 8

0042368-0035218.out:
	prc -hits 1 -align prc 0042368.mod 0035218.mod \
		> 0042368-0035218.out

1plc-1auz.a2m:
	merge_aligns.pl 0042368-0035218.out \
		0042368-1plc.a2m 0035218-1auz.a2m > 1plc-1auz.a2m


When creating SAM alignments, particularly between an HMM and its seed 
sequence, a global alignment (-sw 0) may be preferable in some cases.

To obtain SAM, please go to:

http://www.cse.ucsc.edu/compbio/sam2src/
