Knockout Sudoku, a method for rapidly curating gene disruption collections
- Published
- Accepted
- Subject Areas
- Computational Biology, Genetics, Genomics, Computational Science
- Keywords
- High throughput screening, Systems biology, Combinatorial pooling, Next-generation sequencing
- Copyright
- © 2016 Anzai et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Knockout Sudoku, a method for rapidly curating gene disruption collections. PeerJ Preprints 4:e2294v1 https://doi.org/10.7287/peerj.preprints.2294v1
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.
Author Comment
This is a preprint submission to PeerJ Preprints.