Say I have 5 sequences that are 5 nucleotides long: AAAAA, AAAAC, AAGGC, AGGGG, CCCCC, which represent elements 0 through 4. The similarity matrix would look like this:
100 80 40 20 0
80 100 60 20 20
40 60 100 60 20
20 20 60 100 0
0 20 20 0 100

Because there are 5 pieces of data (0 through 4), the matrix has 25 elements. I already wrote a program that extracts the coordinates and corresponding values of the matrix when this value is greater than 60. Since the matrix is symmetrical, I only extracted values when columns > rows. This is what my program extracts and puts in a text file:

0 1 80
1 2 60
2 3 60

So, there are two clusters. Cluster#1 is 0,1,2,3 and Cluster#2 is 4. Just as data for 4 and 9 are not in the table of the previous example, the data for sequence 4 in this example is not in the table above, which represents the text file that I am working from, but I still have to use these lonely elements as cluster singularities. Anyway, I am working with a huge matrix that is much more complex than this, and I have to figure out a clustering algorithm for it.

 $cluster_60[2]{0} = 2; $cluster_60[0]{1} = 4

Thanks for your help, everyone. I am doing my best to explain my problem. This is a small part of a class project. Its due in over a week. So, I'm not stressed out about it. I don't care about my grade in this class because I am a grad student who really only cares about papers, but I get obsessed when I can't figure something out related to writing code. I use crude perl scripts to analyze biological data and might actually get a paper out of it here soon. I learned Perl over a year ago on my own, and now, my advisor makes me use it everyday and take bioinformatic classes where I have to write scripts. I am really delerious right now because I am tired. The most recent Bill Maher episode with Michael Moore, that Princeton economic nobel laureate, former NY gov Elliot Spitzer, and John Waters was hilarious. I hope that I can become a Perl Monk someday, but I still suck at references and subroutines and have very limited experience with MySQL unlike tye.

In reply to Re^2: Pair-Wise Clustering by cutcopy11
in thread Pair-Wise Clustering by cutcopy11

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