Curtin University Homepage
  • Library
  • Help
    • Admin

    espace - Curtin’s institutional repository

    JavaScript is disabled for your browser. Some features of this site may not work without it.
    View Item 
    • espace Home
    • espace
    • Curtin Research Publications
    • View Item
    • espace Home
    • espace
    • Curtin Research Publications
    • View Item

    Calculating RIP mutation in fungal genomes using RIPCAL

    Access Status
    Fulltext not available
    Authors
    Hane, James
    Date
    2015
    Type
    Book Chapter
    
    Metadata
    Show full item record
    Citation
    Hane, J. 2015. Calculating RIP mutation in fungal genomes using RIPCAL. In Genetic Transformation Systems in Fungi, Volume 2, ed. M. van den Berg & K. Maruthachalam, 69-78. Verlag: Springer.
    Source Title
    Genetic Transformation Systems in Fungi, Volume 2
    ISBN
    9783319105024
    URI
    http://hdl.handle.net/20.500.11937/42312
    Collection
    • Curtin Research Publications
    Abstract

    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.

    Related items

    Showing items related by title, author, creator and subject.

    • Repeat-Induced Point Mutation in Fungi: A Fungal-Specific Endogenous Mutagenesis Process
      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 sequences
      Hane, 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 ...
    Advanced search

    Browse

    Communities & CollectionsIssue DateAuthorTitleSubjectDocument TypeThis CollectionIssue DateAuthorTitleSubjectDocument Type

    My Account

    Admin

    Statistics

    Most Popular ItemsStatistics by CountryMost Popular Authors

    Follow Curtin

    • 
    • 
    • 
    • 
    • 

    CRICOS Provider Code: 00301JABN: 99 143 842 569TEQSA: PRV12158

    Copyright | Disclaimer | Privacy statement | Accessibility

    Curtin would like to pay respect to the Aboriginal and Torres Strait Islander members of our community by acknowledging the traditional owners of the land on which the Perth campus is located, the Whadjuk people of the Nyungar Nation; and on our Kalgoorlie campus, the Wongutha people of the North-Eastern Goldfields.