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. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith–Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid™, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach

Tangible data scanning sonification model

Presented at the 12th International Conference on Auditory Display (ICAD), London, UK, June 20-23, 2006.In this paper we develop a sonification model following the Modelbased Sonification approach that allows to scan high-dimensional data distributions by means of a physical object in the hand of the user. In the sonification model, the user is immersed in a 3D space of invisible but acoustically active objects which can be excited by him. Tangible computing allows to identify the excitation object (e.g. a geometric surface) with a physical object used as controller, and thus creates a strong metaphor for understanding and relating feedback sounds in response to the user's own activity, position and orientation. We explain the technique and our current implementation in detail and give examples at hand of synthetic and real-world data sets

A malleable device with applications to sonification-based data exploration

Presented at the 12th International Conference on Auditory Display (ICAD), London, UK, June 20-23, 2006.This article introduces a novel human computer interaction device, developed in the scope of a Master's Thesis. The device allows continuous localized interaction by providing a malleable interaction surface. Diverse multi-finger as well as multi-handed manipulations can be applied. Furthermore, the device acts as a tangible user interface object, integrated into a tangible computing framework called tDesk. Software to convert the malleable element's shape into an internal surface representation has been developed. Malleable interactions are applied to a new Modelbased Sonification approach for exploratory data analysis. Highdimensional data are acoustically explored via their informative interaction sound in result to the user's excitation

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with Applicatio