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External resources - (No support from the ExPASy Team)Showing 3 records out of 3 total
Continuous time conjunctive Bayesian networks (ct-cbn) are a family of graphical models describing the accumulation of mutations under order constraints. The software allows for the estimation of the network from cross-sectional data, such as mutation profiles of cancer or HIV patients.
keywords: Bayesian network
MARA models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets.
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.
keywords: alignment analysis, Bayesian network, ChIP-seq, hidden markov model (HMM), maximum likelihood, model of evolution, network, next generation sequencing (NGS), sequence alignment, sequence analysis, short sequence alignment, transcription factor binding site, transcription module, transcription regulation