Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets

Table 2 Reduced Amino Acid Alphabets

Scheme	Size	Matrix	Gaps^#	Reference
ML*	4,8,10,15	BL50	12/2	[28]
EB^§	13,11,9,8,5	BL62	11/1	[18]
HSDM*	17	HSDM	19/1	[29]
SDM*	12	SDM	7/1	[29]
GBMR*	4	BL62	11/1	[30]
RANDOM^§	4,4,4	BL62	11/1	This study

Reduced amino acid schemes used in this study.* Substitution matrices for these reduced alphabets were obtained from reference [33]. ^§ BL62 frequency counts were used to derive these substitution matrices using the formula outlined in reference [33]. ^#Gap opening/gap extension penalties used for MSAs in ClustalW2.

ISSN: 1471-2105