RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences.
RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences.
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DOI：
10.1186/1471-2105-9-478
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发表时间：
2008-11-12
影响因子：
3
通讯作者：
Oliver, Richard P.
中科院分区：
文献类型：
--
作者：
Hane, James K.;Oliver, Richard P.
重复诱导点突变（RIP）是一种真菌特异性基因组防御机制，它改变了重复DNA的序列，从而使编码基因失活。重复的DNA序列在交配和减数分裂之间对齐，并且两个序列都经历C：G到T：A的转变。在大多数真菌中，这些转换优先影响CpA二核苷酸，从而改变受影响序列中某些二核苷酸的频率。以前发表的大多数计算机模拟分析仅限于比较puperrin RIP影响序列中RIP前和RIP后二核苷酸的比例-所谓的RIP指数。RIP的分析是显着更多的信息时，比较重复序列的序列比对。然而，真菌研究界缺乏生物信息学工具，用于重复家族的基于重复序列的RIP分析。我们提出了RIPCAL，一个软件工具的RIP真菌基因组DNA重复序列的自动分析，它执行RIP指数和基于重复序列的分析。我们证明了RIPCAL检测RIP的能力，在已知的RIP影响序列粗糙脉孢菌和其他真菌。我们还预测和描绘RIP的存在下，在基因组的Stagonospora nodorum -小麦的Dothideomycete病原体。我们表明，RIP影响了不同的成员的S。nodorum rDNA串联重复的程度不同，这取决于它们的基因组背景。基于RIPCAL指数的方法在全基因组分析中比RIP指数具有相当大的优势。我们证明了它的应用，最近发表的基因组组装的S。结节病。
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. We present 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. 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.
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影响因子：
1.7
作者：
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通讯作者：
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DOI：
10.1007/bf00283420
发表时间：
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期刊：
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