Abstract
One of the most remarkable observations stemming from the sequencing of genomes of diverse species is that the number of protein-coding genes in an organism does not correlate with its overall cellular complexity. Alternative splicing, a key mechanism for generating protein complexity, has been suggested as one of the major explanation for this discrepancy between the number of genes and genome complexity. Determining the extent and importance of alternative splicing required the confluence of critical advances in data acquisition, improved understanding of biological processes and the development of fast and accurate computational analysis tools. Although many model organisms have now been completely sequenced, we are still very far from understanding the exact frequency of alternative splicing from these sequenced genomes.This paper will highlight some recent progress and future challenges for functional genomics and bioinformatics in this rapidly developing area.