Difference between revisions of "Gene tools"
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* <span style="color:#F78F27">'''Sequences:'''</span> DNA and amino acid sequences can be accessed here and saved to fasta file or sent directly to Blast. | * <span style="color:#F78F27">'''Sequences:'''</span> DNA and amino acid sequences can be accessed here and saved to fasta file or sent directly to Blast. | ||
* <span style="color:#C33E96">'''Localization information:'''</span> A graphical representation of the predicted localization of the protein is displayed. Sub-cellular localization prediction was performed in ''Listeria monocytogenes'' EGD-e strain in [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042982 Renier et al. Plos One 2012]. For proteins from a strain different from EGD-e, the localization of its homolog EGD-e protein is shown. | * <span style="color:#C33E96">'''Localization information:'''</span> A graphical representation of the predicted localization of the protein is displayed. Sub-cellular localization prediction was performed in ''Listeria monocytogenes'' EGD-e strain in [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042982 Renier et al. Plos One 2012]. For proteins from a strain different from EGD-e, the localization of its homolog EGD-e protein is shown. | ||
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+ | | [[File:SeqInfo.png|thumb|300px|left|Sequence information panel of the Gene webpage]] | ||
+ | | DNA and amino acid sequences can be accessed here and saved to fasta file or sent directly to Blast. | ||
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Revision as of 10:12, 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.