JunctionViewer: customizable annotation software for repeat-rich genomic regions

Background: Repeat-rich regions such as centromeres receive less attention than their gene-rich euchromatic counterparts because the former are difficult to assemble and analyze. Our objectives were to 1) map all ten centromeres onto the maize genetic map and 2) characterize the sequence features of maize centromeres, each of which spans several megabases of highly repetitive DNA. Repetitive sequences can be mapped using special molecular markers that are based on PCR with primers designed from two unique "repeat junctions". Efficient screening of large amounts of maize genome sequence data for repeat junctions, as well as key centromere sequence features required the development of specific annotation software. Results: We developed JunctionViewer to automate the process of identifying and differentiating closely related centromere repeats and repeat junctions, and to generate graphical displays of these and other features within centromeric sequences. JunctionViewer genera...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Thomas K. Wolfgruber, Gernot G. Presting
• Keywords: BMCBI 2010, Centromeres, Maize, Repeat Junctions