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The explosion in genomic sequence avaliable in public databases has resulted in an unprecedented opportunity for computational whole genome analyses. A number of promising comparative-based approaches have been developed for gene finding, regulatory element discovery and other purposes, and it is clear that these tools will play a fundamental role in analysing the enormous amount of new data that is currently being generated. The synthesis of computationally intensive comparative computational approaches with the requirement for computational scientists. We focus on a few of these challenges, using by way of example the problems of alignment, gene and finding and regulatory element discovery, and discuss the issues that have arisen in attempts to solve these problems in the context of whole genome analysis pipelines.

The computational challenges of applying comparative-based computational methods to whole genomes