Paper Info
Title
Primates and mouse NumtS in the UCSC Genome Browser.
Abstract
NumtS (Nuclear MiTochondrial Sequences) 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.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.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.
Year
DOI
Venue
2012
10.1186/1471-2105-13-S4-S15
BMC Bioinformatics
Keywords
Field
DocType
bioinformatics,genome,mitochondria,algorithms,microarrays
Genome,Population,Biology,Genome browser,Comparative genomics,Nuclear gene,Mitochondrial DNA,Genome evolution,Bioinformatics,Genetics,DNA microarray
Journal
Volume
Issue
ISSN
13
S-4
1471-2105
Citations 
PageRank 
References 
5
0.35
1
Authors
3
Name
Order
Citations
PageRank
Francesco Maria Calabrese1161.96
Domenico Simone2182.63
Marcella Attimonelli316252.64