A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection

Table 1 The effects of a small subtype size

Subtype	Nucleotide	Frequency	Probability
	A	89	99.83%
A	C	0	0.06%
	G	0	0.06%
	T	0	0.06%
	A	392	99.71%
C	C	1	0.27%
	G	0	0.01%
	T	0	0.01%
	A	2	93.18%
K	C	0	2.27%
	G	0	2.27%
	T	0	2.27%

Nucleotide frequencies and the derived emission probabilities for one column in an alignment of HIV-1 Group M sequences without using an information sharing protocol. The emission probabilities are estimated from the nucleotide frequencies using the pseudocounts $\vec{α} = (0.05, 0.05, 0.05, 0.05)$ . We here restrict ourselves to 3 subtypes, A, C, and K.

ISSN: 1471-2105