An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes.
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.
Singh
Abanish
A
Department of Computer Science and Engineering, University of Texas, Arlington, TX 76019, USA. abanish.singh@mavs.uta.edu
Keswani
Umeshkumar
U
Levine
David
D
Feschotte
Cedric
C
D000465:Algorithms; D001483:Base Sequence; D016384:Consensus Sequence; D004251:DNA Transposable Elements / Q000235:genetics*; D056890:Eukaryota; D016678:Genome; D023281:Genomics / Q000379:methods*; D056916:Segmental Duplications, Genomic
D004251:DNA Transposable Elements