In comparative modeling, the quality of amino acid sequence alignment still constitutes a major bottleneck in the generation of high quality models of protein three-dimensional (3D) structures. Substantial efforts have been made to improve alignment quality by revising the substitution matrix, introducing multiple sequences, replacing dynamic programming with hidden Markov models, and incorpora...

MOTIVATION The flexibility in gap cost enjoyed by hidden Markov models (HMMs) is expected to afford them better retrieval accuracy than position-specific scoring matrices (PSSMs). We attempt to quantify the effect of more general gap parameters by separately examining the influence of position- and composition-specific gap scores, as well as by comparing the retrieval accuracy of the PSSMs cons...

The paper focuses on the role of geographical indication in supporting strategies of food safety. Starting from the distinction between generic and specific quality, the article analyses the main factors influencing food safety in cases of geographical indication products, by stressing the importance of traceability systems and biodiversity in securing generic and specific quality. In the secon...

Pursuing the study started by Rigo, Salimov and Vandomme, we use elementary number-theoretic techniques to characterize rotation words having a finite set of abelian returns to all prefixes. We also make the connection between the three gap theorem and the number of semi-abelian returns for Sturmian words, simplifying some arguments developed by Puzynina and Zamboni.

We use a weak Gibbs property and a weak form of specification to derive level-2 large deviations principles for symbolic systems equipped with a large class of reference measures. This has applications to a broad class of coded systems, including β-shifts, S-gap shifts, and their factors. Our techniques are suitable for adaptation beyond the symbolic setting.