Reconstructing the Sequences of Broken Transposable Elements
Abanish Singh, Umeshkumar Keswani, David Levine, Cedric Feschotte and
Nikola Stojanovic
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, wrote 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 the basic approach we used, and
report on the methods for building the consensus sequences of
these transposons.
Index Terms
Algorithms, DNA sequence analysis, graph, repeats, transposons.
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