README.txt file for profile-profile Web site.
(Tabstop=4)

There are three tarball files:

	refaln.tar.gz	Reference alignments.
	scores.tar.gz	Quality scores.
	src.tar.gz		Source code.

This file contains optimized parameters:
	params.txt
	
Reference alignments are in aligned FASTA format:
	Aligned residues are upper-case.
	Unaligned residues are lower-case.
	The gap character is "-".
	The filler character for unaligned positions is ".".

Here is the name of a typical score file:

	pdotp_pb_l_s_o0.2_e0.012_s0.061.cs

The naming convention is:

	<SF>_<TPL1>[_<TPL2>]_l_s_o<GAPOPEN>_e<GAPEXTEND>_s<CENTER>.<SCORETYPE>
	
Fields are:
	SF			Scoring function
	TPL1		Template alignment type (pb=PSI-BLAST, t99=SAM-T99, seed=single sequence)
	GAPOPEN		Affine gap-open parameter
	GAPEXTEND	Affine gap-extend parameter
	CENTER		Center parameter
	SCORETYPE	cs=Cline score, sp=SP (BAliBASE), ps=PS (reverse SP)

The "_l_s" part of the name indicates local-local boundary conditions and simple (i.e., affine)
gap scoring.

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