Calculating RIP mutation in fungal genomes using RIPCAL
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Repeat-induced point mutation (RIP) occurs in some fungal taxa, preferentially mutating C:G nucleotide pairs that reside within repetitive DNA and converting them to T:A. Within the taxon Pezizomycotina, RIP is biased towards mutation of CpA dinucleotides. RIP is an important feature of fungal genomes as its distribution and extent have important implications for genome evolution. Early studies of RIP did not have access to vast amounts of genome sequence information; therefore RIP was measured within one or a handful of repeat sequences using ratios of dinucleotide frequencies. However as whole-genome sequences became available for fungi, it became possible to predict the repeat content of a whole genome and calculate RIP mutation across a large number of sequences from multiple repeat families. The software tool RIPCAL was developed for this purpose and since its release has become widely used in fungal genome analysis pipelines.
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Hane, James; Williams, A.; Taranto, A.; Solomon, P.; Oliver, Richard (2015)Repeat-induced point mutation (RIP) is a form of genome mutation that is targeted towards repeated DNA sequences and which is observed only in certain fungal taxa; the Pezizomycotina (filamentous Ascomycota) and some ...
RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequencesHane, J.; Oliver, Richard (2008)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 ...
In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes.Hane, J.; Oliver, Richard (2010)Background: Repeat-induced point mutation (RIP) is a fungal genome defence mechanism guarding against transposon invasion. RIP mutates the sequence of repeated DNA and over time renders the affected regions unrecognisable ...