To study gene evolution across a wide range of organisms, biologists need accurate tools
for multiple sequence alignment of protein families. Obtaining accurate alignments …

Motivation: An estimated 25% of all eukaryotic proteins contain repeats, which underlines
the importance of duplication for evolving new protein functions. Internal repeats often …

Motivation: The level of sequence conservation between related nucleic acids or proteins
often varies considerably along the sequence. Both regions with high variability (mutational …

Motivation: The pairwise alignment of biological sequences obtained from an algorithm will
in general contain both correct and incorrect parts. Hence, to allow for a valid interpretation …

The score statistics of probabilistic gapped local alignment of random sequences is
investigated both analytically and numerically. The full probabilistic algorithm (eg, the" local" …

Background Computational discovery of transcription factor binding sites (TFBS) is a
challenging but important problem of bioinformatics. In this study, improvement of a Gibbs …

Computational protein structure prediction remains a challenging task in protein
bioinformatics. In the recent years, the importance of template‐based structure prediction is …

 Abstract Sequence alignments are the foundations of life science research, but most
innovation so far focuses on optimal alignments, while information derived from suboptimal …

This paper introduces a simple Sum-over-Paths (SoP) formulation of string edit distances
accounting for all possible alignments between two sequences, and extends related …

The error in protein tertiary structure prediction is unavoidable, but it is not explicitly shown in
most of the current prediction algorithms. Estimated error of a predicted structure is crucial …