Detailed protein sequence alignment based on Spectral Similarity Score (SSS)

Background: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain. Results: Distance matrices of various branches of the human kinome, that is the full complement of human kinases, were developed that matched the phylogenetic tree of the human kinome establishing the efficacy of the global alignment of the algorithm. PKCd and PKCe kinases s...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Kshitiz Gupta, Dina Thomas, S. V. Vidya, K. V. Venkatesh, S. Ramakumar
• Keywords: Algorithm, Amino Acids, BMCBI 2005, Spectral Similarity