computational biology methods and their application to the comparative genomics of endocellular symbiotic bacteria of insects计算生物学方法和他们的应用程序的比较基因组学室内的共生细菌的昆虫.pdfVIP

Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects Jennifer Commins, Christina Toft, and Mario A. Fares Abstract Comparative genomics has become a real tantalizing challenge in the postgenomic era. This fact has been mostly magnified by the plethora of new genomes becoming available in a daily bases. The overwhelming list of new genomes to compare has pushed the field of bioinformatics and computational biology forward toward the design and development of methods capable of identifying patterns in a sea of swamping data noise. Despite many advances made in such endeavor, the ever-lasting annoying exceptions to the general patterns remain to pose difficulties in generalizing methods for comparative genomics. In this review, we discuss the different tools devised to undertake the challenge of comparative genomics and some of the exceptions that compromise the generality of such methods. We focus on endosymbiotic bacteria of insects because of their genomic dynamics peculiarities when compared to free-living organisms. Keywords: Comparative Genomics, Orthologs search, BLAST, Functional Categories, Genomics Dynamics. 1. Genomes, Genomes, and More Genomes The emergence of genome information has overwhelmed our efforts to analyze the unexpected amount of data generated during the last two decades. As an example, today (February, 2009), there are 438 complete microbial genomes and 17 in draft in the J. Craig Venter Institute, Comprehensive Microbial Resource website (URL: /tigr-scripts/CMR/CmrHomePage. cgi) considering that this is only a single resource we estimate that Shulin Li (ed.), Biological Procedures Online, Volume 11, Number 1 © to the auth