An algorithm to find all identical internal sequence repeats

Banerjee, Nirjhar ; Chidambarathanu, N. ; Michael, Daliah ; Balakrishnan, N. ; Sekar, K. (2008) An algorithm to find all identical internal sequence repeats Current Science, 95 (2). pp. 188-195. ISSN 0011-3891

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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

Item Type:Article
Source:Copyright of this article belongs to Current Science Association.
Keywords:Dynamic Programing; Evolutionary Studies; Internal Sequence Repeats; Structure-function Relationship
ID Code:66572
Deposited On:24 Oct 2011 08:11
Last Modified:18 May 2016 14:03

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