Thesis writeup section tied states.

Simulating on different input encodings, final encoding for the std
grammar.
PCA implemented for input encoding dimension reduction.
(1) Test different input representations all using Non-negative matrix
	factorisation or Principle Component Analysis for input encoding
	dimension reduction
	--> msa profile (created)
	--> msa + hyydrophobic moment profiles (created)
	--> single seq + msa profile (created)

(2) Different grammars, mixtures, and window sizes
	--> tied at mixture level not state level
	--> different mixture numbers (1,3)
	--> window sizes (15,19,31)

(3) PSICOV 
	--> contact map estimation
	--> look for significant local correlation as most people only search
		for non-local correlation for beta-strands
	--> data stored on server at /gluster/data/tmb_maps.tgz