RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences

Background: Repeat-induced point mutation (RIP) is a fungal-specific genome defence mechanism that alters the sequences of repetitive DNA, thereby inactivating coding genes. Repeated DNA sequences align between mating and meiosis and both sequences undergo C:G to T:A transitions. In most fungi these transitions preferentially affect CpA di-nucleotides thus altering the frequency of certain di-nucleotides in the affected sequences. The majority of previously published in silico analyses were limited to the comparison of ratios of pre- and post-RIP di-nucleotides in putatively RIP-affected sequences

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: James K. Hane, Richard P. Oliver
• Keywords: Alignment-based Rip Analysis, BMCBI 2008, RIP Indices, Sequences