通过计算机反转重复诱导点突变（RIP），可以确定重复家族的起源，并揭示被掩盖的重复基因。
In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes.
机构信息
Faculty of Health Sciences, Murdoch University, Perth, Western Australia, 6150, Australia.
出版信息
BMC Genomics. 2010 Nov 24;11:655. doi: 10.1186/1471-2164-11-655.
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.
背景
重复诱导点突变（RIP）是一种真菌基因组防御机制，可防止转座子入侵。RIP 会使重复 DNA 的序列发生突变，随着时间的推移，受影响的区域将无法通过 BLAST 等相似性搜索工具识别。
结果
DeRIP 是一种新开发的软件工具，用于在 RIP 发生之前预测 RIP 突变区域的原始序列。在本研究中，我们将 deRIP 应用于小麦病原体禾旋孢腔菌 SN15 的基因组中，并预测了几个以前未表征的重复 DNA 类别的起源。
结论
经过 deRIP 后，鉴定出了 5 种新的转座子重复类和 4 种内源性基因重复类。deRIP 过程是真菌基因组学的一种新工具，有助于鉴定和理解真菌重复 DNA 的作用和起源。DeRIP 是开源的，并作为 RIPCAL 套件的一部分可在 http://www.sourceforge.net/projects/ripcal 上获得。
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