a model of the statistical power of comparative genome sequence analysis一个模型的统计比较基因组序列分析的力量.pdfVIP

Open access, freely available online PLoS BIOLOGY A Model of the Statistical Power of Comparative Genome Sequence Analysis Sean R. Eddy Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America Comparative genome sequence analysis is powerful, but sequencing genomes is expensive. It is desirable to be able to predict how many genomes are needed for comparative genomics, and at what evolutionary distances. Here I describe a simple mathematical model for the common problem of identifying conserved sequences. The model leads to some useful rules of thumb. For a given evolutionary distance, the number of comparative genomes needed for a constant level of statistical stringency in identifying conserved regions scales inversely with the size of the conserved feature to be detected. At short evolutionary distances, the number of comparative genomes required also scales inversely with distance. These scaling behaviors provide some intuition for future comparative genome sequencing needs, such as the proposed use of ‘‘phylogenetic shadowing’’ methods using closely related comparative genomes, and the feasibility of high-resolution detection of small conserved features. Citation: Eddy SR (2005) A model of the statistical power of comparative genome sequence analysis. PLoS Biol 3(1): e10. total neutral branch length in the phylogeny ( P d ), because Introduction i i the probability that a neutral site has no changes in any Comparative g