Comparative Genomic Analysis of Neisseria

All the genomic analyses were performed within MicroScope using embedded software. Whole-genome comparisons of gene content (using the mentioned cutoffs) were done using the PhyloProfile Synteny functionality [19 (link)], which combines BLASTP, BBH and/or synteny results. Graphical representation of whole-genome syntenies were generated using LinePlot functionality [19 (link)]. Graphical circular representation of the strain 8013 genome with transposon insertions was generated using the CGView software [56 (link)]. Characterization of the sulfate reduction pathway in Neisseria strains colonizing the nasopharynx was done using metabolic pathway predictions built with the Pathway Tools software [57 (link)]. GIs of putative horizontally transferred genes were identified in each N. meningitidis clinical isolate using the Genomic Island functionality tool [19 (link)]. This tool combines detection of synteny break points in the query genome in comparison with closely related genomes, searches for mobility genes, tRNA and direct repeats (if any) at the borders of the synteny break points and finally searches for compositional bias in the query genome.

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Rusniok C., Vallenet D., Floquet S., Ewles H., Mouzé-Soulama C., Brown D., Lajus A., Buchrieser C., Médigue C., Glaser P, & Pelicic V. (2009). NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis. Genome Biology, 10(10), R110.

Publication 2009

Direct repeats Genes Genome Genomic island Insertions Meningitidis n Microscope Mobility Nasopharynx Neisseria Strains Sulfate Synteny Transposon Trna

Corresponding Organization :

Other organizations : Institut Pasteur, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de la Recherche Scientifique, Inserm, Université Paris Cité, Imperial College London

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