Weight Matrix Research

1. Introduction of Weight Matrices

   1. Description of Weight Matrices:

      A scoring system is one of the tools needed to manipulate the degree of similarity between sequences. Weight matrices are the most commonly used scoring system for protein sequences similarity analysis. There are more than 20 kinds of weight matrices which can be divided into two large groups. One group is based on genetic code exchange (base substitution) and other group is based on amino acid structure or properties.

      The development and classification of weight matrices:

      
      

      THE DEVELOPMENT OF WEIGHT MATRICES

      Year	Author	Name of Matrix	Detail Method
      1956	UPM	Unitary Protein Matrix	1 for matching
      			0 for other aa exchanges.
      1966	Fitch	MNR Matrix	Minimum mumber base changes required
      1972	McLachlan	AAA(Alternative Amino Acid)Matrix	Structural homologies between proteins to observe substitution
      1972	Dayhoff	PAM-MDM Matrix	Log-Odds Matrix
      1974	Seller	GCM(Genetic Code Matrix)	base changes	0	1	2	3
      			score	4	2	1	0
      1974	Grantham	RSF Matrix	Physico-chemical characters:polarity, volume and composition
      1979	Miyata	Distance Matrix	Based on amino acid polarity and volume
      1979	Doolittle	Intutive Structure Genetic Matrix	Account for genetic coding feature and side chain properties
      1985	Feng	SGM (Structure Genetic Matrix)	(1)structure similarities of aa side chain properties
      			(2)substitution of amino acid
      1986	Levin	RBO (Secondary Structur Similarity Matrix)	From X-ray crystallography data
      1987	Rao	EMPAR Matrix	PAM Matrix and 5 physical properties	(1)alpha-helix
      				(2)beta strand
      				(3)reverse-turn properties
      				(4)polarity
      				(5)hydrophobicity
      1988	Riser	For three-dimensional structure
      1990	Johnson	Log-Odds Matrix	Sequence distance matrix		For three-dimensional structure
      			and Structure Matrix
      1991	Altschul	Relative Entropy Substitution Matrix
      1992	Henikoff and Henikoff	BLOSUM Matrix	Sequence and Structurr Matrix
      1992	Gonnet	GCB Matrix
      1992	Jones	JTT Matrix
      1993	Henikoff and Henikoff	STR Matrix	Sequence comparison clustered at identical percentage level
      1994	Benner	Benner Matrix	Based on	genetic distance
      				and PAM Matrix
      1994	Benner	Benner Matrix for secondary structure	DSSP (Define Secondary Structure for X-ray crystallography)
      			PAM Matrix

   

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2. BLOSUM Matrix

3. LEVIN'S Matrix

4. Create A New Secondary Structure Weight Matrix

   
   

5. Summary