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GrainGenes Reference Report: BBI-9-478

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Reference	BBI-9-478
Title	RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences.
Journal	BMC Bioinformatics
Year	2008
Volume	9
Pages	478
Author	Hane JK Oliver RP
Abstract	ABSTRACT: 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 - so-called RIP indices. The analysis of RIP is significantly more informative when comparing sequence alignments of repeated sequences. There is, however, a dearth of bioinformatics tools available to the fungal research community for alignment-based RIP analysis of repeat families. RESULTS: We present RIPCAL (www.sourceforge.net/projects/ripcal), a software tool for the automated analysis of RIP in fungal genomic DNA repeats, which performs both RIP index and alignment-based analyses. We demonstrate the ability of RIPCAL to detect RIP within known RIP-affected sequences of Neurospora crassa and other fungi. We also predict and delineate the presence of RIP in the genome of Stagonospora nodorum - a Dothideomycete pathogen of wheat. We show that RIP has affected different members of the S. nodorum rDNA tandem repeat to different extents depending on their genomic contexts. CONCLUSIONS: The RIPCAL alignment-based method has considerable advantages over RIP indices for the analysis of whole genomes. We demonstrate its application to the recently published genome assembly of S. nodorum.
External Databases	http://dx.doi.org/10.1186/1471-2105-9-478

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