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移动基因组发现器:用于在计算机上和通过实验发现细菌基因组岛的网络工具。

MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands.

作者信息

Ou Hong-Yu, He Xinyi, Harrison Ewan M, Kulasekara Bridget R, Thani Ali Bin, Kadioglu Aras, Lory Stephen, Hinton Jay C D, Barer Michael R, Deng Zixin, Rajakumar Kumar

机构信息

Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, PR China.

出版信息

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W97-W104. doi: 10.1093/nar/gkm380. Epub 2007 May 30.

Abstract

MobilomeFINDER (http://mml.sjtu.edu.cn/MobilomeFINDER) is an interactive online tool that facilitates bacterial genomic island or 'mobile genome' (mobilome) discovery; it integrates the ArrayOme and tRNAcc software packages. ArrayOme utilizes a microarray-derived comparative genomic hybridization input data set to generate 'inferred contigs' produced by merging adjacent genes classified as 'present'. Collectively these 'fragments' represent a hypothetical 'microarray-visualized genome (MVG)'. ArrayOme permits recognition of discordances between physical genome and MVG sizes, thereby enabling identification of strains rich in microarray-elusive novel genes. Individual tRNAcc tools facilitate automated identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites and other integration hotspots in closely related sequenced genomes. Accessory tools facilitate design of hotspot-flanking primers for in silico and/or wet-science-based interrogation of cognate loci in unsequenced strains and analysis of islands for features suggestive of foreign origins; island-specific and genome-contextual features are tabulated and represented in schematic and graphical forms. To date we have used MobilomeFINDER to analyse several Enterobacteriaceae, Pseudomonas aeruginosa and Streptococcus suis genomes. MobilomeFINDER enables high-throughput island identification and characterization through increased exploitation of emerging sequence data and PCR-based profiling of unsequenced test strains; subsequent targeted yeast recombination-based capture permits full-length sequencing and detailed functional studies of novel genomic islands.

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/901a/1933208/56a17b74a1d7/gkm380f1.jpg

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