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.



Please be patient, computing results ...


Please be patient, computing genomic loci analysis ...

Your genomic loci analysis is ready!