Type: Analyzing ProtoNet

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.

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.

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

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