Cartoon of a multiple sequence alignment and its mapping to a Markov random field. Shown in the figure is a cartoon figure of a multiple sequence alignment (MSA) and a corresponding Markov random field (MRF). There is one node in the MRF for each column in the MSA. The column-wise conservation statistics in the MSA are encoded by node potentials (Φi). Similarly, the co-variation statistics in the MSA (e.g., between columns 1 and 4) are encoded by edge potentials (φ1,4) in the MRF. The lack of an edge between two nodes means that the corresponding columns are conditionally independent.
Moitra et al. BMC Biophysics 2012 5:13 doi:10.1186/2046-1682-5-13