Software |
Informations |
Outputs |
Sources |
Biological retrieval |
This software is completely invisible to the user; it performs queries on our database that merge data from UniprotKB and NCBI-Gene to retrieve the maximum biological information about proteins in the dataset. Biological information includes identifiers (genes, accession number, gi, protein ID), function, chromosome location, orthologs, functional annotation, and protein sequences (FASTA file). |
Excel file / FASTA file |
UniprotKB / NCBI-Gene |
Ontologies |
This program selects GO from the QuickGO server for each protein (GO identifier, name, function and functional group). The selection depends on the evidence code (IEA codes are unselected in basic analysis, but can be selected in custom analysis) and the curator review of the annotation. It provides over- and under-represented terms to identify the most relevant, specific terms associated with the uploaded list. Within a GO, the script compares the number of genes or proteins from the dataset to the total number of gene products declared in the AmiGO database to provide a coverage frequency, and thus to identify the most common pathways associated to a dataset. |
Diagrams / Excel files / GO Tree network |
Quick GO / AmiGO / UniprotKB |
Peptide Prediction |
This program runs a local version of SignalP 4.1. It uses the sequences of input proteins (FASTA file) to identify a signal peptide type: secretory protein, non-secretory protein, or transmembrane peptides. The program also checks if a protein is annotated by GO related to a secretory function. |
Excel file |
CBS-SignalP 4.1 |
Protein-protein Interactions (PPi) |
This program searches protein-protein interactions between proteins on the input file. Several databases are available and the program performs queries on each of these bases using the Psicquic service. The results are analysed directly on the server, and Psicquic shows interactions verified experimentally and sorts them depending on their experimental interaction detection method.
Database:
APID ChEMBL BioGrid IntAct DIP MPIDB MINT MatrixDB iRefIndex BIND Interoporc STRING Reactome-FIs Reactome InnateDB-IMEx MolCon BindingDB I2D-IMEx I2D DrugBank GeneMANIA Spike TopFind VirHostNet UniProt MBInfo mentha InnateDB bhf-ucl HPIDb BAR EBI-GOA-nonIntAct |
Excel files / PPi networks |
PSI-Psicquic |