GIPS: A Software Guide to Sequencing-Based Direct Gene Cloning in Forward Genetics Studies. Issue 4 (3rd February 2016)

• Record Type: Journal Article
• Authors: Hu, Han; Wang, Weitao; Zhu, Zhongxu; Zhu, Jianhua; Tan, Deyong; Zhou, Zhipeng; Mao, Chuanzao; Chen, Xin
• Is Part Of: Plant physiology. Volume 170:Issue 4(2016)
• Page Start: 1929
• Page End: 1934
• Publication Date: 2016-02-03
• Subjects: Plant physiology -- Periodicals; Botany -- Periodicals; Periodicals; Electronic journals; 571.2
• DOI: 10.1104/pp.15.01327
• Languages: English
• ISSNs: 0032-0889

Abstract

Abstract : A software tool incorporating a range of experimental and data analysis choices in a sequencing-based forward genetics study aids in the design of an optimal procedure for gene identification. Abstract: 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.