Fig. 1

ParasoR overview illustration. A target sequence fragment is assigned to K computational nodes, and \(d{\alpha ^{h}_{k}}\) is stored in external memory in the Divide procedure to solve the dependency problem that exists around the ends of a given fragment. In the Connect procedure, exact local fold changes Δ α are computed by the summation of \(d{\alpha ^{h}_{k}}\) for each pairing pattern at the left end of the assigned fragment. In the computation of expected values, a variety of measures are available using the DP variables whose magnitudes are bounded independently of N, such as u(k,l), Δ α, and Δ β