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This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2011

Open Access Research

Primates and mouse NumtS in the UCSC Genome Browser

Francesco Maria Calabrese, Domenico Simone and Marcella Attimonelli*

Author Affiliations

Dipartimento di Bioscienze, Biotecnologie e Scienze Farmacologiche, Università di Bari, Bari, 70126, Italy

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BMC Bioinformatics 2012, 13(Suppl 4):S15  doi:10.1186/1471-2105-13-S4-S15

Published: 28 March 2012

Abstract

Background

NumtS (

    N
uclear
    M
i
    T
ochondrial
    S
equences) are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized the nuclear genome. Accurate mapping of NumtS avoids contamination during mtDNA PCR amplification, thus supplying reliable bases for detecting false heteroplasmies. In addition, since they commonly populate mammalian genomes (especially primates) and are polymorphic, in terms of presence/absence and content of SNPs, they may be used as evolutionary markers in intra- and inter-species population analyses.

Results

The need for an exhaustive NumtS annotation led us to produce the Reference Human NumtS compilation, followed, as reported in this paper, by those for chimpanzee, rhesus macaque and mouse ones. Identification of NumtS inside the UCSC Genome Browser and their inter-species comparison required the design and the implementation of NumtS tracks, starting from the compilation data. NumtS retrieval through the UCSC Genome Browser, in the species examined, is now feasible at a glance.

Conclusions

Analyses involving NumtS tracks, together with other genome element tracks publicly available at the UCSC Genome Browser, can provide deep insight into genome evolution and comparative genomics, thus improving studies dealing with the mechanisms that drove the generation of NumtS. In addition, the NumtS tracks constitute a useful tool in the design of mitochondrial DNA primers.