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This Week in Nucleic Acids Research: Dec 20, 2017

Researchers from the US, France, and the UK report on a database that brings together reference plant ontologies with species-specific information on everything from plant phenotypes to gene ontology, taxonomic, and experimental data. The resource, which stemmed from the Planteome project, currently contains expression, gene function, and other data for plants from 95 taxa. The team has also set its sights on other Planteome developments, including a plant stress ontology reference and a web-based gene annotation and curation tool called Planteome Noctua. "The data collected from these efforts will be shared semantically with sequencing projects, sequence archives, and publishers of scientific literature for useful integration and consistency," the authors note.

A team from Japan explores local sequence rearrangements in the human genome using a high-throughput analytical pipeline focused on finding insertions, intrachromosomal shifts, and other rearrangements contained within long sequence reads. Using this probability-based approach, the team assessed tens of millions of MinION nanopore and Pacific Biosciences long read sequences generated for the NA12878 human cell line, identifying sequence errors and authentic local rearrangements. Based on such results, the authors say their probability-based pipeline made it possible to put together "a catalog of local rearrangements in one human cell line, and show which rearrangement patterns occur."

Stanford University and University of Pennsylvania researchers present an algorithm for finding large rearrangements in cancer genomes that have been tackled with barcode-linked sequence reads. The team paired this ZoomX algorithm with barcode-linked reads produced using 10X Genomics library prep methods, search for inversions, deletions, and other rearrangements spanning sequences as nearby as 200,000 bases and as broad as several million bases. In a proof-of-principle analysis, the investigators applied ZoomX to linked read data generated for the NA12878 human cell line using 10,000 base scan grids. Their results suggest that the approach can detect large rearrangements in this line and in tumor samples with mixed cellularity.