An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes Online publication date: Wed, 10-Mar-2010
by Abanish Singh, Umeshkumar Keswani, David Levine, Cedric Feschotte, Nikola Stojanovic
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 6, No. 2, 2010
Abstract: Interspersed repeats, mostly resulting from the activity and accumulation of transposable elements, occupy a significant fraction of many eukaryotic genomes. More than half of human genomic sequence consists of known repeats, however a very large part has not yet been associated with neither repetitive structures nor functional units. We have postulated that most of the seemingly unique content of mammalian genomes is also a result of transposon activity, written software to look for weak signals which would help us reconstruct the ancient elements with substantially mutated copies, and integrated it into a system for de novo identification and classification of interspersed repeats. In this manuscript we describe our approach, and report on our methods for building the consensus sequences of these transposons.
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