The parameters for computing the GNN and associated files are summarized in the table.
|Input % Co-Occurrence||20|
|Number of SSN clusters||61|
|Number of SSN singletons||40|
|SSN sequence source||UniRef90|
|Number of SSN (meta)nodes||1,048|
|Number of accession IDs in SSN||7,555|
Each cluster in the submitted SSN has been identified and assigned a unique number and color. Node attributes for "Neighbor Pfam Families" and "Neighbor InterPro Families" have been added.
|# Nodes||# Edges||File Size (Zipped MB)|
GNNs provide a representation of the neighboring Pfam families for each SSN cluster identified in the colored SSN. To be displayed, neighboring Pfams families must be detected in the specified window and at a co-occurrence frequency higher than the specified minimum.
Each hub-node in the network represents a SSN cluster. The spoke nodes represent Pfam families that have been identified as neighbors of the sequences from the center hub.
|File Size (Zipped MB)|
Each hub-node in the network represents a Pfam family identified as a neighbor. The spokes nodes represent SSN clusters that identified the Pfam family from the center hub.
|File Size (Zipped MB)|
Diagrams representing genomic regions around the genes encoded for the sequences from the submitted SSN are generated. All genes present in the specified window can be visualized (no minimal co-occurrence frequency filter or neighborhood size threshold is applied). Diagram data can be downloaded in .sqlite file format for later review in the View Saved Diagrams tab.
|Action||File Size (Zipped MB)|
|Opens GND explorer in a new tab.|
|Diagram data for later review||63|
|Neighbor Pfam domain fusions at specified minimal co-occurrence frequency||2 MB|
|Neighbor Pfam domains at specified minimal co-occurrence frequency||2 MB|
|Neighbor Pfam domain fusions at 0% minimal co-occurrence frequency||4 MB|
|Neighbor Pfam domains at 0% minimal co-occurrence frequency||5 MB|
|Neighbors without Pfam assigned||<1 MB|
|No matches/no neighbors file||<1 MB|
|Pfam family/cluster co-occurrence table file||1 MB|
|GNN hub cluster sequence count file||<1 MB|
|Cluster size file||<1 MB|
|SwissProt annotations per SSN cluster||<1 MB|
|SwissProt annotations by singleton||<1 MB|
Please change parameters or select a new file to upload before refiltering.
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