Protein-Protein Physical Interaction Network Mapper
If you are looking for the standalone version of Nascent please visit our Downloads page.
Nascent is a protein-protein physical interaction network construction tool based on gene names and sequence similarity.
Our program searches for proteins of source organism which are in physical interaction by the IntAct database.
- When the "construct by gene names" option is selected, those proteins are assigned to their respective gene names. We use these gene names to make a correspondence between the source and the target organisms making a predicted protein-protein physical interaction network for the target organism.
- When the "construct by sequence similarity" option is selected, we use protein sequence similarities to make a correspondence between the source and the target organism making a predicted protein-protein physical interaction network for the target organism.
Write into the appropriate boxes both the NCBI Taxonomy ID of the source and target organism; an interactive search system helps you to this, if you do not know that ID, but know the latin name of the species (e.g., Mus musculus for the mouse). Check the "include subtree" field if the interaction data need to be generated for all the descendants of the species in the phylogenetic tree. Then choose the output image option. After pressing the "Schedule job" button your request will be inserted into a queue. Please be patient as it may take some time for our server to get to your request, this time strongly depends on on the layout chosen, and it varies from 5 seconds to even 10-20 minutes for graphs with several thousand vertices and a complex force-based layout. Progress is monitored in a log window in detail. The result will be some links in the log window leading to files containing a list of the predicted edges of the target organism, a link to a Java applet for manipulating the graph, and also a JPG image for quick viewing. The nodes of edges will be displayed as UniProtKB AC numbers.
Note: Result and log files are stored for 5 days, and can be accessed without re-constructing the network by bookmarking the query-page.
Tutorial video about online and desktop versions
You can use this tool and the related database freely, no registration is necessary. You are kindly required, however, to cite the following publication in any subsequent work of yours, using the NASCENT tool:
Daniel Banky, Rafael Ordog, Vince Grolmusz: NASCENT: An automatic protein interaction network generation tool for non-model organisms Bioinformation 3(8)(2009), www.bioinformation.net
The use of this tool is subject to the following conditions; if you do not agree these conditions, please do not use this tool and the accompanying program:
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