Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be - Motivation: The mutation of amino acids often impacts protein function and structure. Mutations without negative effect sustain evolutionary pressure.

Active site prediction using evolutionary and structural information - Motivation: The identification of catalytic residues is a key step in understanding the function of enzymes. While a variety of computational methods have been developed for this task, accuracies have remained fairly low.

RNAsnoop: efficient target prediction for H/ACA snoRNAs - Motivation: Small nucleolar RNAs are an abundant class of non-coding RNAs that guide chemical modifications of rRNAs, snRNAs and some mRNAs. In the case of many ‘orphan’ snoRNAs, the targeted nucleotides remain unknown, however.

ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes - Motivation: Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences.

Xper2: introducing e-taxonomy - Motivation: Computer Aided Identification systems provide users with the resources to relate morpho-anatomic observations with taxa names and to subsequently access other knowledge about the organisms.

Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization - DNA microarray measurements are susceptible to error caused by non-specific hybridization between a probe and a target (cross-hybridization), or between two targets (bulk-hybridization).

A calibrated diversity assay for nucleic acid libraries using DiStRO--a Diversity Standard of Random Oligonucleotides - We have determined diversities exceeding 1012 different sequences in an annealing and melting assay using synthetic randomized oligonucleotides as a standard.

Validation of double digest selective label database for sequenced prokaryotic genomes - Summary: A database for simulation of double digest selective label (DDSL) typing technique has been created and validated against a sequenced strain (Salmonella enterica serovar Typhimurium strain LT2).

DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data - Summary: DNA copy number alterations (CNA) frequently underlie gene expression changes by increasing or decreasing gene dosage.

Fortunately, R package developers finally got to the problem of parallel computations. An excerpt (below) from a recent Bioinformatics article is a good illustration.