Gene tools
Contents
Gene webpage
The gene webpage can be accessed either from the home webpage of the Listeriomics website or by double-clicking on a genome in the genomic webpage.
General organization
| Chromosome selection
Here one can select a specific genome among the 50 Listeria strains available. Then one has to select a chromosome. In Listeria species, in general the first one is a circular chromosome and the second one is a plasmid. With a star are indicated genomes for which transcriptomic datasets are available. |
| Gene search and selection
In this list, all the genes available for a specific chromosome are displayed. One can search for a gene locus, a gene name, or even key words which can be found in the annotation of each gene. A click on an element of the list will display all related information on the Gene information panel. |
| Omics panel selection
For each Listeria gene four different information panels are available. The first one gives all general information about the position of the gene, possible annotated function, nucleotide sequence and amino-acid sequence. The second panel provides an instant view of the conservation of a specific gene in other Listeria strains. It dynamically displays on the Listeria phylogram presence of absence of homolog to the selected gene in each existing Listeria strain. It also displays a summary table of all homologs with their similarity percentages and amino acid sequences. One can then create a multi-alignment file of the homologs. A third panel uses the expression atlas to show in which transcriptomics datasets the selected gene is differently expressed. The cut-off on the Log(Fold Change) value for detecting such elements can be changed by the user. Finally the fourth panel displays every proteomics dataset in which the protein coded by the selected gene has been detected. |
| Gene information panel
All |
How-to access gene annotation ?
| Gene panel
For each |
Is my gene conserved ?
| Gene panel
For each |
Is my gene transcribed ?
| Gene panel
For each |
Is my gene translated ?
| Gene panel
For each |
