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Assembly and characterization of novel Alu inserts detected from next-generation sequencing data.

ABSTRACT: Repetitive elements generally, and Alu inserts specifically are a large contributor to the recent evolution of the human genome. By assembling the sequences of novel Alu inserts using their respective subfamily consensus sequences as references, we found an exponential decay in the Alu subfamily 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 reference Alu sources of a subset of the novel Alus, of which 85% were previously shown to be active. We also evaluate relationships between the loci of the novel inserts and their inferred sources.

SUBMITTER: Mustafa H

PROVIDER: S-EPMC4589995 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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Assembly and characterization of novel Alu inserts detected from next-generation sequencing data.

Mustafa Harun H David Matei M Brudno Michael M

Mobile genetic elements 20141001 5

Repetitive elements generally, and Alu inserts specifically are a large contributor to the recent evolution of the human genome. By assembling the sequences of novel Alu inserts using their respective subfamily consensus sequences as references, we found an exponential decay in the Alu subfamily 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 refere ...[more]

PMID: 26442170

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