RepeatAround: A software tool for finding and visualizing repeats in circular genomes and its application to a human mtDNA database
Ana Goios, José Meirinhos, Ricardo Rocha, Ricardo Lopes, António Amorim and Luísa Pereira
2006
Abstract
RepeatAround is a Windows based software tool
designed to find
direct repeats,
inverted repeats,
mirror repeats and
complementary repeats, from 3 to 64
bp length, in circular genomes. It processes input files directly
extracted from GenBank database, providing visualisation of the
repeats location in the genomic structure, so that for instance, in
most mtDNAs the user can check if the repeats are located in coding or
non-coding region (and in the first case in which gene), and how far
apart the repeat pair(s) are. Besides the visual tool, it provides
other outputs in a spreadsheet containing information on the number
and location of the repeats, facilitating graphic analyses. Several
genomes can be inputed simultaneously, for phylogenetic comparison
purposes. Other capabilities of the software are the generation of
random circular genomes, for statistical evaluation of comparison
between observed repeats distributions with their shuffled
counterparts, as well as the search for specific motifs, allowing an
easy confirmation of repeats flanking a newly detected
rearrangement. As an example of the programme's applications we
analysed the Direct Repeats distribution in a large human mtDNA
database. Results showed that Direct Repeats, even the larger ones,
are evenly distributed among the human mtDNA haplogroups, enabling us
to state that, based only on the repetitive motifs, no haplogroup is
particularly more or less prone to mtDNA macrodeletions.
Bibtex
@Article{goios-mitochondrion06,
author = {A. Goios and J. Meirinhos and R. Rocha and R. Lopes and A. Amorim and L. Pereira},
title = {{RepeatAround: A software tool for finding and visualizing repeats in circular genomes and
its application to a human mtDNA database}},
journal = {Mitochondrion Journal},
pages = {218--224},
volume = {6},
number = {4},
year = {2006},
}
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