Consistent Quantification of Complex Dynamics via a Novel Statistical Complexity Measure.

Natural systems often show complex dynamics. The quantification of such complex dynamics is an important step in, e.g.

PFASUM: a substitution matrix from Pfam structural alignments.

Background: Detecting homologous protein sequences and computing multiple sequence alignments (MSA) are fundamental tasks in molecular bioinformatics. These tasks usually require a substitution matrix for modeling evolutionary substitution events derived from a set of aligned sequences. Over the last years, the known sequence space increased drastically and several publications demonstrated that this can lead to significantly better performing matrices.

Addressing inaccuracies in BLOSUM computation improves homology search performance.

Background: BLOSUM matrices belong to the most commonly used substitution matrix series for protein homology search and sequence alignments since their publication in 1992. In 2008, Styczynski et al. discovered miscalculations in the clustering step of the matrix computation.