Background: Structure-dependent substitution matrices increase the accuracy of sequence alignments when the 3D structure of one sequence is known, and are successful e.g. in fold ...
—Inferring latent structures from observations helps to model and possibly also understand underlying data generating processes. A rich class of latent structures are the latent ...
Motivation: Mapping of remote evolutionary links is a classic computational problem of much interest. Relating protein families allows for functional and structural inference on u...
We describe and demonstrate the effectiveness of a method of predicting protein secondary structures, sheet regions in particular, using a class of stochastic tree grammars as rep...
Background: In vertebrates, a large part of gene transcriptional regulation is operated by cisregulatory modules. These modules are believed to be regulating much of the tissue-sp...