Genomic tools

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General Organization[edit]

Thanks to Genomics button on the top banner, one can access the genomic webpage which is designed to browse through every complete genome available and access strain name, serotype, lineage, and isolation information, along with a complete phylogram of the Listeria strains. By double clicking on a strain the list of annotated genes will appear in a new summary panel.

Printscreen of the genomics webpage of the Listeriomics website
Listeria species reference phylogenomic tree

Nucleic acid alignments of ortholog gene families were concatenated into a single super-alignment. This super-alignment was used to compute a Maximum Likelihood tree using FastTree2, a parallelized and optimized software to build Maximum Likelihood trees. The following parameters were used: the Generalized time-reversible model (GTR) was chosen, the exhaustive search mode was selected to obtain a more accurate reconstruction, NNI and SPR heuristics were used to browse the tree space and BIONJ weighting was chosen to join events during tree space browsing. Support analyses were performed using Shimodaira Hasegawa test (SH) associated with 1000 resampling steps of site likelihood.

List of 83 Listeria genomes with strain information available

For each genome, information about serotype, lineage and the origin of strain isolation were retrieved when possible. By double-clicking on a genome in the table, the gene panel will open and show the annotation available for selected genome.

Genomics database[edit]

83 complete Listeria genomes available on NCBI RefSeq and GenBank databases were downloaded and integrated into our database.