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ProtoNet: Site Map.

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Type: Analyzing ProtoNet

Query: Cluster Distance Distributions (full service is available in advanced mode only)

Here the user enters the ProtoNet ID of two clusters and selects a clustering algorithm.

Here the user enters the ProtoNet ID of two clusters and selects a clustering algorithm

First, let us define some necessary terminology:

  • An intra-cluster protein pair is defined as a pair of proteins, consisting of two proteins from the same cluster.
  • An inter-cluster protein pair is defined as a pair of proteins, consisting of one protein from each cluster.
  • The distance between the 2 proteins in such a pair is defined as the E-score of the BLAST between them.
NOTE: that all distances greater than 100 are ignored.

So, entering the 2 clusters produces 3 distance distribution histograms:

  1. The distribution of distances between all intra-cluster pairs of proteins, in the 1st cluster
  2. The distribution of distances between all intra-cluster pairs of proteins, in the 2nd cluster
  3. The distribution of distances between all inter-cluster pairs of proteins.
NOTE: that the 2 clusters don't necessarily have to pass the threshold to be analyzed in this section.

Histograms

Clicking "Proceed" on any of the histograms will yield the corresponding pairs' distance matrix.

Matrix

Clicking on a given entry in the matrix will yield, in a new window, the BLAST results for the given protein pair.

 


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