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ProtoNet: Site Map.

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Type: Vertical perspective

Query: Get cluster card

This page is accessed by clicking on Get cluster card. Entering a cluster number will open the appropriate "cluster card" page (if it exists).

 

The top of the Cluster Page displays the cluster and the position in the tree.
cluster card

 

Next we see general information about the cluster.

General Info

Size 74 proteins
Number of Solved structures (in PDB) 2 proteins, 2 PDB's
Number of proteins without Prosite ID 26
Number of Hypothetical proteins 8
Number of Fragments 7
Average length and standard deviation of proteins 74.4 20.8
Number of clusters at ProtoLevel at creation * get data
Number of leaves at ProtoLevel at creation * get data
ProtoLevel at creation * 0.0184476255804496
ProtoLevel at termination * 27.6559354134473
Lifetime * 27.6374877878668
Fraction of "parent" cluster 95%
Click on "get data" to obtain the data where it is appropriate.
* - this feature available in Advanced mode only

 

The tree at the top right of the page displays the immediate "neighborhood" of the cluster in the ProtoNet tree. cluster in tree

 

This tree depicts the clustering process graphically, where each node represents a cluster. When mousing over a cluster, a tooltip appears showing cluster size (amount of proteins in the cluster), cluster ID, parent ID, and cluster name. The cluster name is defined as the keyword that best matches the proteins of the cluster, if one exists. Note that the tree that is displayed is only a subtree showing the immediate "neighborhood" of the cluster. To see more of the tree, use the Steps Up and Steps Down options of "ProtoBrowser".

ProtoBrowser

 

links to the "Keyword Appearances" page and to the "PANDORA"

Below this tree is a link to the "Keyword Appearances" page, describing the keywords of a specific type that are assigned to the proteins of the cluster.
[ See "Keyword Appearances" page of the Site Map ]

 

Finally, there is a link to send the cluster's proteins to be viewed in PANDORA, in order to study the proteins' biology through their annotations.**
[ About PANDORA ]

** - this feature is currently only available in Advanced mode, for clustering "Arithmetic 40.28"

 

 

 

 

 


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