Please be patient, computing GO enrichment ...
Your GO enrichment is ready!
Please be patient, computing KEGG pathway enrichment ...
Your KEGG enrichment is ready!
Please be patient, computing common IDs conversion ...
Your common IDs conversion is ready!
Please be patient, computing tree ...
Press the Show Orthogroup Evolution button to
visualize the expansions and contractions in orthogroup size across
the different branches of the species tree. Only orthogroups that have
significantly undergone these processes are shown. Note that only orthogroups
present at the root of the tree are analyzed. Orthogroups present in
less than 10 species or with a great difference in gene copies between species
are also excluded.
Please be patient, reconstructing ancestors ...
Next, click on the Show Gene Selection for Pfam button,
select the desired proteins from the tree and click
on the Show Pfam Domains button to determine their PFAM domains. A table with
the domains of each protein and their positions will be displayed,
as well as a plot showing the same information. Warning: this process may take
a long time in the case of selecting many proteins.
Please be patient, identifying domains ...
Next, click on the Show Gene Selection for MSA button,
select the desired proteins from the tree and click
on the Compute MSA button to show the alignment. The alignment is shown
as text, including the consensus sequence. For a graphical representation with
the different aminoacids colored according to their chemical nature, click on
the download button. The aligned sequences can also be download as a FASTA file.
Warning: This process (specially the colored download) may take a long time in the case
of selecting many proteins.
Please be patient, aligning sequences ...
Click on the button to select the genes of
interest from the tree and select the ontology type to display
the GO terms associated with those genes. After pressing the
Show GO terms button, the results are displayed in tabular form and are
accompanied by a GO association plot (each node is a GO and an
edge is drawn between two nodes if a gene has both terms) and
a treeplot showing the hierarchy of the identified terms and
their summary.
Please be patient, computing GO terms ...
Click on the button to select the genes of
interest from the tree and press the Show KEGG information
button to show the results. These include a table showing the
KEGG Orthology IDs, indicating how many and which of the selected
proteins correspond to each ID. In addition, the application performs
an enrichment in KEGG pathways from the identified KOs and allows
for the plotting of these pathways with the genes mapped onto them,
using a selector to choose the pathway in case several enriched ones exist.
Warning: this process may take a long time in the case of selecting many
proteins. Attempts to plot large pathways will produce an error, only
more specific ones are supported i.e. Carbon metabolism will
return an error while Biotin metabolism will not
Please be patient, exploring pathways ...
In the text box, type the search term to query your
bibliographic information, i.e., CCA1. Then select one of the 4 search
modes: Normal returns the entities containing the term, Exact returns
those that are identical, Alias returns all aliases associated with the
term and Substring returns all those containing a given string. Associations
found in the literature are returned in tabular form, with links to the papers
from which the information was extracted. This functionality is based on
PlantConnectome, to extend this analysis, it is recommended to use
https://connectome.plant.tools/.
Please be patient, searching literature ...
Select the desired organism and press the button to choose a genome
(the amino acid sequences corresponding o the main transcript of each gene) used in the
development of the tool with the ID considered for each sequence. Then press the download button to download
it. To change the organism, select the new one and press again the Acess genome files button
to update the genome before downloading.
To avoid mismatches between theentered gene
IDs and those used by the application, in this tab you can
paste the sequence of the protein to be analyzed and select the working
species. The result will be a single-element
table with the best identity result, indicating the similarity of
the protein entered with the protein used by the application. The ID
shown in the table can be then used for performing the analysis.