12、国外大学研究所收集sanger研究所chapter4.pdfVIP

Chapter 4Chapter 4 CChhaapptterer 44 Resolving the structure of Genomic Islandstructure of Genomic Islands Resolving the s Resolving the sesolving the structure of Genomic Islandstructure of Genomic Islands R 4.14.1 Introduction Introduction 4.4.11 IntroductionIntroduction Horizontally acquired DNA sequences that con n functionally related genes with limited phylogenetic distribution, i.e. present in some bacterial genomes while being absent from closely related ones, are often referred to as genomic islands (GIs). The location of those mobile elements often correlates with distinct structural features such as tRNA genes, direct repeats (DRs) and mobility genes, which has lead to a definition of the GI structure that includes these features (Table 4.1), (Hacker et al., 1997; Hacker and Kaper, 2000; Schmidt and Hensel, 2004). GIs present in Gram-positive bacteria may differ structurally from those present in Gram-negative bacteria; overall they do not exhibit specific junction sites (e.g. DRs), they are rarely inserted adjacent to RNA loci and they are often stably integrated in the host genome due to the lack of mobility genes (Hacker et al., 1997). Several web-based suites exploit the GI structural definition (Table 4.1) with the aim of implementing and automating the in silico prediction of genomic regions that share some or all of the GI-related signatures; those regions are subsequently annotated as novel GIs. For example Islander (Mantri and Williams, 2004) and IslandPath (Hsiao et al., 2003), two web-based suites, combine and overlap several GI-related features trying to predict genomic regions as close as possible to the GI structural definition. Although a large number of mobile elements fall well within the GI definition, there are several concerns about the struct