title: In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes.
abstract: 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 by similarity search tools such as BLAST.
  
  
  RESULTS
  DeRIP is a new software tool developed to predict the original sequence of a RIP-mutated region prior to the occurrence of RIP. In this study, we apply deRIP to the genome of the wheat pathogen Stagonospora nodorum SN15 and predict the origin of several previously uncharacterised classes of repetitive DNA.
  
  
  CONCLUSIONS
  Five new classes of transposon repeats and four classes of endogenous gene repeats were identified after deRIP. The deRIP process is a new tool for fungal genomics that facilitates the identification and understanding of the role and origin of fungal repetitive DNA. DeRIP is open-source and is available as part of the RIPCAL suite at http://www.sourceforge.net/projects/ripcal.
authors.affiliation: Faculty of Health Sciences, Murdoch University, Perth, Western Australia, 6150, Australia.
authors.forename: James K
authors.initials: JK
authors.lastname: Hane
authors.forename: Richard P
authors.initials: RP
authors.lastname: Oliver
mesh_terms: D001203:Ascomycota / Q000235:genetics*; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D018628:Gene Dosage; D020131:Genes, Duplicate / Q000235:genetics*; D005800:Genes, Fungal / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010802:Phylogeny; D017354:Point Mutation / Q000235:genetics*; D053484:RecQ Helicases / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D004251:DNA Transposable Elements; D004271:DNA, Fungal; D053484:RecQ Helicases