Tutorial computentional Challenges in comparative Genomics

Computational Challengesin Comparative GenomicsA TutorialBERNARD M.E. MORETWITH WEBB C. MILLER, PAVEL A. PEVZNER, AND DAVID SANKOFF1 IntroductionComparative approaches have long been a mainstay of biology and medicine. Inpart, this is due to necessity: many organisms and systems are difficult to pro-cure or to maintain in the laboratory, while ethical concerns have prevented ex-perimentation with humans and are reducing experimentation with higher mam-mals. Thus, in particular, much of what we know about humans has been learnedthrough animal models. More importantly, comparative approaches embody anevolutionary approach to biology—and that, ever since Darwin, is what has en-abled biologists to make sense out of the extremely complex systems they study.The great pioneer Theodore Dobzhansky famously wrote an essay entitled “Noth-ing makes sense in biology except in the light of evolution,” in which he arguesthat the large amount of data collected by field and bench biologists can onlyreveal their structure through an analysis based on evolution. Since evolution-ary processes can only be understood through the comparison of various productsof these processes, comparative approaches must form the foundation of any bi-ological research method. The case is even more compelling today than whenDobzhansky wrote his essay: with the advent of high-throughput instruments formolecular biology and now for other aspects of biology and the life sciences,the amount ...