RepeatAround: A software tool for finding and visualizing repeats in circular genomes and its application to a human mtDNA database

• Type: Article in International Scientific Journal
• Date: 2006

Authors

Ana Goios (Author) Other; Jose Meirinhos (Author) Other; Ricardo Rocha (Author) FCUP; Ricardo Lopes (Author) FCUP; Antonio Amorim (Author) FCUP; Luisa Pereira (Author) Other

Journal

Title: Mitochondrion

Vol. 6

Pages: 218-224

ISSN: 1567-7249

Publisher: Elsevier

Indexing

ISI Web of Knowledge - 10 Citations

Scopus - 11 Citations

Scientific classification

FOS: Natural sciences > Biological sciences

Other information

Authenticus ID: P-004-J9R

DOI: 10.1016/j.mito.2006.06.001

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 7