Background: Probabilistic models for sequence comparison (such as hidden Markov models and pair hidden Markov models for proteins and mRNAs, or their context-free grammar counterp...
We consider the problem of finding a matching between two sets of features, given complex relations among them, going beyond pairwise. Each feature set is modeled by a hypergraph ...
This paper presents a new approach to site-directed recombination, swapping combinations of selected discontiguous fragments from a source protein in place of corresponding fragmen...
We show how to build hierarchical, reduced-rank representation for large stochastic matrices and use this representation to design an efficient algorithm for computing the largest...
Phylogenetic hidden Markov models (phylo-HMMs) have recently been proposed as a means for addressing a multispecies version of the ab initio gene prediction problem. These models ...