The number of amino acid sequences is increasing very rapidly in the protein databases like Swiss-Prot, Uniprot, PIR and others, but the structure of only some
amino acid sequences are found in the Protein Data Bank. Thus, an important problem in genomics is automatically clustering homologous protein sequences
when only sequence information is available. Here, we use graph theoretic techniques for clustering amino acid sequences. A similarity graph is defined and
clusters in that graph correspond to connected subgraphs. Cluster analysis seeks grouping of amino acid sequences into subsets based on distance or similarity
score between pairs of sequences. Our goal is to find disjoint subsets, called clusters, such that two criteria are satisfied: homogeneity: sequences in the same
cluster are highly similar to each other; and separation: sequences in different clusters have low similarity to each other. We tested our method on several subsets
of SCOP (Structural Classification of proteins) database, a gold standard for protein structure classification. The results show that for a given set of proteins the
number of clusters we obtained is close to the superfamilies in that set; there are fewer singeltons; and the method correctly groups most remote homologs.