Knockout Sudoku, a method for rapidly curating gene disruption collections
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Abstract
Knockout Sudoku is a method for the construction of whole-genome knockout collections for a wide range of microorganisms with as little as 3 weeks of dedicated labor and at a cost of approximately $10,000. The method uses manual 4-dimensional combinatorial pooling, next-generation sequencing and a Bayesian inference algorithm to rapidly process and then accurately annotate the extremely large progenitor transposon insertion mutant collections needed to achieve saturating coverage of complex microbial genomes. Here we present a protocol for the generation, combinatorial pooling and annotation of highly oversampled progenitor collections and their subsequent algorithmically guided condensation and curation into high-quality collections suitable for rapid genetic screening and gene discovery.
Cite this as
2016. Knockout Sudoku, a method for rapidly curating gene disruption collections. PeerJ Preprints 4:e2294v1 https://doi.org/10.7287/peerj.preprints.2294v1Author comment
This is a preprint submission to PeerJ Preprints.
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Additional Information
Competing Interests
The authors are seeking patent protection for the probabilistic reconstruction algorithm used in the Knockout Sudoku method.
Author Contributions
Isao A Anzai performed the experiments, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Lev Shaket conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.
Oluwakemi Adesina performed the experiments, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Michael Baym conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper, conceived Knockout Sudoku method.
Buz Barstow conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper, conceived Knockout Sudoku method.
Data Deposition
The following information was supplied regarding data availability:
The KOSUDOKU package and sample input and output data are available at https://github.com/buzbarstow/kosudoku.
Funding
This work was supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and Princeton University startup funds to Buz Barstow. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
