MobilomeFINDER -- web-based tools for in silico and experimental discovery of bacterial genomic islands
What you can do:
An interactive online tool that facilitates bacterial genomic island or 'mobile genome' (mobilome) discovery.
Highlights:
- MobilomeFINDER 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.
Keywords:
- Enterobacteriaceae
- Gene Expression Regulation
- Bacterial Genome
- Genomic Islands
- Pseudomonas aeruginosa
- Streptococcus suis
- bacterial genome island
Literature & Tutorials:
This record last updated: 06-05-2008