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An algorithm to find all identical internal sequence repeats

Banerjee, Nirjhar and Chidambarathanu, N and Michael, Daliah and Balakrishnan, N and Sekar, K (2008) An algorithm to find all identical internal sequence repeats. In: Current Science, 95 (2). pp. 188-195.

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Abstract

Proteins containing amino acid repeats are considered to be of great importance in evolutionary studies. The principal mechanism of formation of amino acid repeats is by the duplication or recombination of genes. Thus, repeats are found in both nucleotide and protein sequences. In proteins, repeats are involved in protein-protein interactions as well as in binding to other ligands such as DNA and RNA. The study of internal sequence repeats would be helpful to scientists in various fields, including structural biology, enzymology, phylogenetics, genomics and proteomics. Hence an algorithm (Finding All Internal Repeats, FAIR) has been designed utilizing the concepts of dynamic programing to identify the repeats. The proposed algorithm is a faster and more efficient method to detect internal sequence repeats in both protein and nucleotide sequences, than those found in the literature. The algorithm has been implemented in $C^{++}$ and a web-based computing engine, IdentSeek, has been developed to make FAIR accessible to the scientific community. IdentSeek produces a clear, detailed result (including the location of the repeat in the sequence and its length), which can be accessed through the world wide web at the URL http://bioserver1.physics.iisc.ernet.in/ident/.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Indian Academy of Sciences.
Keywords: Dynamic programing, evolutionary studies;internal sequence repeats;structure–function relationship.
Department/Centre: Division of Information Sciences > Supercomputer Education & Research Centre
Division of Information Sciences > BioInformatics Centre
Date Deposited: 13 Oct 2008 06:14
Last Modified: 19 Sep 2010 04:50
URI: http://eprints.iisc.ernet.in/id/eprint/16015

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