I need to find dissimilar proteins. Looking through the PDB I found the weekly BLASTClust results of proteins that are 30% similar. However, I do not know if protein A in cluster 1 is guaranteed to be less than 30% similar to protein B in cluster 2.
The best and only documentation I can find for BLASTClust is here (link).
The program begins with pairwise matches and places a sequence in a cluster if the sequence matches at least one sequence already in the cluster.
That's good, but consider a set of three proteins (A, B, and C). A is 40% similar to B and 40% similar to C. B is 20% similar to C. Say that the algorithm places B in cluster 1 and then C in cluster 2 as they are dissimilar. What happens when it tries to place A? Because A is similar to both B and C will they be joined into one cluster (this would be the best result for me) or is A just placed into one cluster even though it is similar to a protein in another cluster?