Difference between revisions of "Gene tools"
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* General information: The position of the gene, possible annotated function, nucleotide sequence and amino-acid sequence. | * General information: The position of the gene, possible annotated function, nucleotide sequence and amino-acid sequence. | ||
* Gene conservation in other ''Listeria'' strains : It dynamically displays on the Listeria phylogram presence or 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. | * Gene conservation in other ''Listeria'' strains : It dynamically displays on the Listeria phylogram presence or 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. | ||
+ | * Synteny viewer to display conservation of whole group of genes in different 'Listeria' strains | ||
* Expression atlas: It shows 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. | * Expression atlas: It shows 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. | ||
* Protein atlas: It displays every proteomics dataset in which the protein coded by the selected gene has been detected. | * Protein atlas: It displays every proteomics dataset in which the protein coded by the selected gene has been detected. |
Revision as of 10:25, 19 October 2016
Contents
General organization
The gene webpage can be accessed either from the home webpage of Listeriomics website or by double-clicking on a genome in the genomic webpage.
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 selection panel
For each Listeria gene four different information panels are available.
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Gene information panel
The panel in which all information will be displayed |
How-to access gene annotation?
Click on General information on the Omics selection panel
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DNA and amino acid sequences can be accessed here and saved to fasta file or sent directly to Blast. |
Is my gene conserved?
Click on Homologs on the Omics selection panel
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A synteny viewer is available to see the conservation of whole groups of genes. It uses SynTView architecture [1]. |
Is my gene transcribed?
Click on Expression Atlas on the Omics selection panel
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Is my gene translated?
Click on Proteomes on the Omics selection panel
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- ↑ Lechat P., Souche E., Moszer I. 2013. SynTView - an interactive multi-view genome browser for next-generation comparative microorganism genomics. BMC Bioinformatics. 2013 Sep 22;14:277. doi: 10.1186/1471-2105-14-277.