Skip to main content
Fig. 1 | BMC Bioinformatics

Fig. 1

From: General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?

Fig. 1

Genuine stochastic evolutionary model vs. HMM (or transducer). a Probability density calculation via a genuine stochastic evolutionary model. Each sequence state is represented as an array of sites (boxes). Sites to be deleted are shaded in red or magenta. Inserted sites are shaded in blue or cyan. The s I and s F , respectively, denote the initial and final states. The s ν (ν = 1, 2, 3) is an intermediate state. (The “P[…]” denotes a probability, the “p[…]” denotes a probability density.) b A pairwise alignment (PWA) between the initial (I) and final (F) states resulted from the indel process in panel a. The C i (i = 1, …, 10) labels the alignment column below. c Probability calculation via a HMM (or a transducer). It is a priori unclear whether or how the methods in panels a and c are related with each other. For clarity, residue states and substitutions were omitted. (Note that the equation in panel a is merely a rough expression to give a broad idea on the issue. Rigorous expressions will be given in Results and discussion.) Panels a and b of this figure were adapted from panels B and F of Fig. 1 of [32]

Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us