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

@article{citeulike:3507433, 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 http://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.CONCLUSION: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.}, author = {Hane, James and Oliver, Richard}, citeulike-article-id = {3507433}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-9-478}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19014496}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19014496}, comment = {id:\#50}, day = {12}, doi = {10.1186/1471-2105-9-478}, issn = {1471-2105}, journal = {BMC Bioinformatics}, keywords = {alignment, fungal\_genomes, genome, rip, tool}, month = {November}, number = {1}, pages = {478+}, posted-at = {2009-10-30 17:07:17}, priority = {2}, title = {RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences}, url = {http://dx.doi.org/10.1186/1471-2105-9-478}, volume = {9}, year = {2008} }

TY - JOUR ID - citeulike:3507433 L3 - citeulike-article-id:3507433 N2 - 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 http://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.CONCLUSION: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. IS - 1 JF - BMC Bioinformatics SN - 1471-2105 TI - RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences VL - 9 SP - 478 KW - alignment KW - fungal_genomes KW - genome KW - rip KW - tool N1 - id:#50 AU - Hane, James AU - Oliver, Richard PY - 2008/11/12/ UR - http://dx.doi.org/10.1186/1471-2105-9-478 ER -