Exploration of multivariate analysis in microbial coding sequence modeling

BMC Bioinformatics

Table 2 The number of probabilities to be estimated in an IMM

Sequence type	*k =* 0	*k =* 1	*k =* 2	*k =* 3	*k =* 4	*k =* 5
DNA	12	60	252	1020	4092	16380
Protein	20	420	8420	168420	3368420	67368420
Codon	61	3782	230763	14076604	858672905	52379047266

The columns represent the number of transition probabilities to be estimated with an Interpolated Markov model from k = 0 to k = 5, while the rows designate the different sequence types (DNA, codon and protein). The number of probabilities in a k^th order IMM corresponds to the number of regression coefficients for the k + 1 word frequencies in the CPPLS method.

ISSN: 1471-2105