ITR: Computational Techniques for Applied Bioinformatics

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This award provides support for a collaborative project involving two computer scientists and a plant geneticist who will develop new methods, efficient algorithms, and software tools for several important problems in the field of bioinformatics. This supported work includes research into computational paradigms such as quartet methods, interactive systems, and approximation algorithms as applied to the evolutionary analysis of gene sequences, gene duplication, and horizontal transfer events in the genomes of chloroplasts, a DNA-containing organelle found in all plants. Additional studies will examine the information content of genomes by improving and testing a recently developed sequence entropy estimator and a distance metric for genomic sequences. Work in this area will include the application of the improved methods to sequence data from the genomes of mitochondria, viruses, chloroplasts and bacteria. Other efforts will address the important problem of simultaneous multiple sequence alignment and evolutionary tree reconstruction. The multiple sequence alignment approaches to be developed are based on the use of conserved blocks that have few or no gaps, and multiple alignments within a constant band. Work in a fourth area will develop efficient algorithms for computing short and long interspersed nuclear elements (SINES and LINES) in genomic sequences of lengths up to billions of nucleotides. Because of the large amounts of data that must be analyzed, this will require the development or adaptation of appropriate external memory algorithms. Biological, biomedical and pharmaceutical research is undergoing a major revolution as new analytical technologies produce unprecedented amounts of genetic data. The exploration of this information is critically dependent upon the development of advanced computational and software techniques for data analysis, storage and retrieval. From this dependency, a new interdisciplinary research field, bioinformatics (or computational molecular biology) has emerged in recent years. The work supported through this award is expected to make both fundamental and applied contributions to the field. The fundamental research will explore and explicate new ideas and methods for solving algorithmic problems in bioinformatics and the applied research will involve the development and evaluation of software tools in the practice of plant genomics. Although the efforts are aimed at improving the understanding of the evolution of chloroplast genomes, the approaches should be readily extensible to analysis of all other genomes.