High performance computational tools for motif discovery

The research described in this paper highlights a fruitful interplay between biology and computation. The sequencing of complete genomes from multiple organisms has revealed that most differences in organism complexity are due to elements of gene regulation that reside in the non protein coding portions of genes. Both within and between species, transcription factor binding sites and the proteins that recognize them govern the activity of cellular pathways that mediate adaptive responses and survival. Experimental identification of these regulatory elements is by nature a slow process. The availability of complete genomic sequences, however, opens the door for computational methods to predict binding sites and expedite our understanding of gene regulation at a genomic level. Just as with traditional experimental approaches, the computational identification of the molecular factors that control a gene’s expression level has been problematic. As a case in point, the identification of putative motifs, which is the subject of this paper, is a challenging combinatorial task. For it, powerful new motif finding algorithms and high performance implementations are described. Heavy use is made of graph algorithms, some of which are exceedingly computationally intensive and involve the use of emergent mathematical methods. An approach to fully dynamic load balancing is developed in order to make effective use of highly parallel platforms. Key Words and Phrases Computational genomics, elucidation of cis-regulatory elements, parallel algorithms for molecular sequence analysis, protein binding and mRNA transcriptio