GIPS: A Software Guide to Sequencing-Based Direct Gene Cloning in Forward Genetics Studies
GIPS: A Software Guide to Sequencing-Based Direct Gene Cloning in Forward Genetics Studies
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GIPS：正向遗传学研究中基于测序的直接基因克隆软件指南
DOI：
10.1104/pp.15.01327
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发表时间：
2016-04-01
期刊：
影响因子：
7.4
通讯作者：
Chen, Xin
中科院分区：
文献类型：
--
作者：
Hu, Han;Wang, Weitao;Chen, Xin
通过表型测序的基因鉴定（GIPS）软件在一个综合的概率框架内考虑了基于测序的正向遗传学研究中的一系列实验和分析选择，这使得可以从相同表型的几个不相关突变体的测序中直接克隆基因，而无需创建分离群体。GIPS估计四个测量值以帮助优化分析程序，如下：（1）报告真实表型相关基因的机会;（2）可能报告的随机基因的预期数量;（3）每个候选基因与表型相关的显著性;以及（4）如果没有基因被报告或如果所有候选基因都没有通过验证，则违反孟德尔假设的显著性。GIPS的使用说明与鉴定的水稻（水稻）基因，上位抑制磷酸盐2突变体的表型从测序三个无关的甲基磺酸乙酯突变体。GIPS可在https://github.com/synergy-zju/gips/wiki上获得，并附有用户手册和分析示例。
The Gene Identification via Phenotype Sequencing (GIPS) software considers a range of experimental and analysis choices in sequencing-based forward genetics studies within an integrated probabilistic framework, which enables direct gene cloning from the sequencing of several unrelated mutants of the same phenotype without the need to create segregation populations. GIPS estimates four measurements to help optimize an analysis procedure as follows: (1) the chance of reporting the true phenotype-associated gene; (2) the expected number of random genes that may be reported; (3) the significance of each candidate gene's association with the phenotype; and (4) the significance of violating the Mendelian assumption if no gene is reported or if all candidate genes have failed validation. The usage of GIPS is illustrated with the identification of a rice (Oryza sativa) gene that epistatically suppresses the phenotype of the phosphate2 mutant from sequencing three unrelated ethyl methanesulfonate mutants. GIPS is available at https://github.com/synergy-zju/gips/wiki with the user manual and an analysis example.