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RepEx: Repeat extractor for biological sequences

Gurusaran, M and Ravella, Dheeraj and Sekar, K (2013) RepEx: Repeat extractor for biological sequences. In: GENOMICS, 102 (4). pp. 403-408.

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Official URL: http://dx.doi.org/10.1016/j.ygeno.2013.07.005


Genomic sequences are far from being random but are made up of systematically ordered and information rich patterns. These repeated sequence patterns have been vastly utilized for their fundamental importance in understanding the genome function and organization. To this end, a comprehensive toolkit, RepEx, has been developed which extracts repeat (inverted, everted and mirror) patterns from the given genome sequence(s) without any constraints. The toolkit can also be used to fetch the inverted repeats present in the protein sequence (s). Further, it is capable of extracting exact and degenerate repeats with a user defined spacer intervals. It is remarkably more precise and sensitive when compared to the existing tools. An example with comprehensive case studies and a performance evaluation of the proposed toolkit has been presented to authenticate its efficiency and accuracy. (C) 2013 Elsevier Inc. All rights reserved.

Item Type: Journal Article
Publication: GENOMICS
Additional Information: Copyright for their article belongs to ACADEMIC PRESS INC ELSEVIER SCIENCE, 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA
Keywords: Software; Inverted repeat sequences; Palindromic repeat sequences; Amino acid repeat sequence; Repetitive sequences; Genome
Department/Centre: Division of Interdisciplinary Sciences > Supercomputer Education & Research Centre
Date Deposited: 12 Dec 2013 12:20
Last Modified: 12 Dec 2013 12:20
URI: http://eprints.iisc.ac.in/id/eprint/47893

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