A small tool written in Java for cluster analysis of sequences.
The problem of finding groups of co-regulated genes across a number of microarray experiments is quite similar to the problem of finding groups of homologous proteins in a large dataset. In both cases we have huge amounts of data and are looking for those few genes that show some kind of significant similarity.
Putative co-regulation as well as putative homology are generally inferred from similarities in the feature set of a gene. In the first case the feature set consists of the expression levels across the experiments, in the second case of the amino-acid sequences of the proteins.
A certain similarity is also apparent when you look at the graphs generated for either protein sequence data or microarray data. Get CLANS and take it for a spin to see what it can actually do for you!