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Genes Cells. 2014 Jun;19(6):517-27. doi: 10.1111/gtc.12151. Epub 2014 Apr 28.

Mudi, a web tool for identifying mutations by bioinformatics analysis of whole-genome sequence.

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1
Genome Informatics Laboratory, National Institute of Genetics, Mishima, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.

Abstract

In forward genetics, identification of mutations is a time-consuming and laborious process. Modern whole-genome sequencing, coupled with bioinformatics analysis, has enabled fast and cost-effective mutation identification. However, for many experimental researchers, bioinformatics analysis is still a difficult aspect of whole-genome sequencing. To address this issue, we developed a browser-accessible and easy-to-use bioinformatics tool called Mutation discovery (Mudi; http://naoii.nig.ac.jp/mudi_top.html), which enables 'one-click' identification of causative mutations from whole-genome sequence data. In this study, we optimized Mudi for pooled-linkage analysis aimed at identifying mutants in yeast model systems. After raw sequencing data are uploaded, Mudi performs sequential analysis, including mapping, detection of variant alleles, filtering and removal of background polymorphisms, prioritization, and annotation. In an example study of suppressor mutants of ptr1-1 in the fission yeast Schizosaccharomyces pombe, pooled-linkage analysis with Mudi identified mip1(+) , a component of Target of Rapamycin Complex 1 (TORC1), as a novel component involved in RNA interference (RNAi)-related cell-cycle control. The accessibility of Mudi will accelerate systematic mutation analysis in forward genetics.

PMID:
24766403
DOI:
10.1111/gtc.12151
[Indexed for MEDLINE]
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