Research in Bioinformatics and Semantic Web
The MoBIoS (Molecular Biological Information System) library forms the core of a next generation database management system for life science data. The java-based library utilizes metric space indexing techniques to enable fast retrieval of sequences and mass spectra signatures.
We have created several parallel search algorithms using a technique named exclusion and metric space indexing to perform quick searches. Metric space indexing is a technique that allows a set of data points to be partitioned into easily searchable regions in a tree form, based solely on the distances between the points. This approach works well within the bioinformatics domain allowing complicated, and normally expensive, distance functions to be created and still obtain quick results.
RNA sequence alignment
This project aims to develop a pipeline to generate high quality and large-scale RNA multiple sequence alignments incorporating structure and phylogeny information. We have implemented a lightweight program that performs structure-based pairwise alignment in a fast fashion with high accuracy.