title: Assembly and characterization of novelAluinserts detected from next-generation sequencing data.
abstract: Repetitive elements generally, andAluinserts specifically are a large contributor to the recent evolution of the human genome. By assembling the sequences of novelAluinserts using their respective subfamily consensus sequences as references, we found an exponential decay in theAlusubfamily call enrichment with increased number of sequence variants (Pearson correlation [Formula: see text], [Formula: see text]). By mapping the sequences of these inserts to a human reference genome, we infer the referenceAlusources of a subset of the novelAlus, of which 85% were previously shown to be active. We also evaluate relationships between the loci of the novel inserts and their inferred sources.
authors.affiliation: Department of Computer Science; University of Toronto ; Toronto, Canada.
authors.forename: Harun
authors.initials: H
authors.lastname: Mustafa
authors.affiliation: Department of Computer Science; University of Toronto ; Toronto, Canada.
authors.forename: Matei
authors.initials: M
authors.lastname: David
authors.affiliation: Department of Computer Science; University of Toronto ; Toronto, Canada ; Centre for Computational Medicine; Hospital for Sick Children ; Toronto, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Brudno
keywords: Alu; Hi-C; SINE; SNP; chromosomal conformation capture; retrotransposon