Commercially viable biofuel crops are vital to reducing greenhouse gas emissions, and a new tool developed by the Center for Advanced Bioenergy and Bioproducts Innovation should accelerate their development -; as well as genetic editing advances overall.
CROPSR, the first open-source software tool for genome-wide design and evaluation of guide RNA (gRNA) sequences for CRISPR experiments, created by scientists at CABBI, a Department of Energy-funded Bioenergy Research Center (BRC). The genome-wide approach significantly shortens the time required to design a CRISPR experiment, reducing the challenge of working with crops and accelerating gRNA sequence design, evaluation, and validation, according to the study published in BMC Bioinformatics.
“CROPSR provides the scientific community with new methods and a new workflow for performing CRISPR/Cas9 knockout experiments,” said CROPSR developer Hans Müller Paul, a molecular biologist and Ph.D. student with co-author Matthew Hudson, Professor of Crop Sciences at the University of Illinois Urbana-Champaign. “We hope that the new software will accelerate discovery and reduce the number of failed experiments.”
CROPSR developer Hans Müller Paul, a molecular biologist and Ph.D. student with co-author Matthew Hudson, Professor of Crop Sciences at the University of Illinois Urbana-Champaign
To better meet the needs of crop geneticists, the team built software that lifts restrictions imposed by other packages on design and evaluation of gRNA sequences, the guides used to locate targeted genetic material. Team members also developed a new machine learning model that would not avoid guides for repetitive genomic regions often found in plants, a problem with existing tools. The CROPSR scoring model provided much more accurate predictions, even in non-crop genomes, the authors said.
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