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Ultrafast search of all deposited bacterial and viral genomic data

Bradley, Phelim ; den Bakker, Henk C ; Rocha, Eduardo P C ; McVean, Gil ; Iqbal, Zamin

Nature biotechnology, 2019-02, Vol.37 (2), p.152-159 [Periódico revisado por pares]

United States: Nature Publishing Group

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Título:
Ultrafast search of all deposited bacterial and viral genomic data
Autor: Bradley, Phelim ; den Bakker, Henk C ; Rocha, Eduardo P C ; McVean, Gil ; Iqbal, Zamin
Assuntos: Algorithms ; Antibiotic resistance ; Antibiotics ; Bacteria ; Chromosome Mapping ; Computational Biology - methods ; Computer applications ; Data structures ; Databases, Factual ; Datasets ; Drug Resistance, Bacterial - genetics ; Epidemiology ; Escherichia coli - genetics ; Escherichia coli Proteins - genetics ; False Positive Reactions ; Genome, Bacterial ; Genome, Viral ; Genomics ; Genotype ; Membrane Proteins - genetics ; Microorganisms ; Models, Statistical ; Molecular Epidemiology ; Mycobacterium - genetics ; Nucleotide sequence ; Phylogeny ; Plasmids ; Plasmids - genetics ; Programming Languages ; Salmonella - genetics ; Searching ; Sequence Analysis, DNA ; Staphylococcus - genetics ; Streptococcus - genetics ; Transferases (Other Substituted Phosphate Groups) - genetics
É parte de: Nature biotechnology, 2019-02, Vol.37 (2), p.152-159
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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Descrição: Exponentially increasing amounts of unprocessed bacterial and viral genomic sequence data are stored in the global archives. The ability to query these data for sequence search terms would facilitate both basic research and applications such as real-time genomic epidemiology and surveillance. However, this is not possible with current methods. To solve this problem, we combine knowledge of microbial population genomics with computational methods devised for web search to produce a searchable data structure named BItsliced Genomic Signature Index (BIGSI). We indexed the entire global corpus of 447,833 bacterial and viral whole-genome sequence datasets using four orders of magnitude less storage than previous methods. We applied our BIGSI search function to rapidly find resistance genes MCR-1, MCR-2, and MCR-3, determine the host-range of 2,827 plasmids, and quantify antibiotic resistance in archived datasets. Our index can grow incrementally as new (unprocessed or assembled) sequence datasets are deposited and can scale to millions of datasets.
Editor: United States: Nature Publishing Group
Idioma: Inglês

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Ultrafast search of all deposited bacterial and viral genomic data

Bradley, Phelim ; den Bakker, Henk C ; Rocha, Eduardo P C ; McVean, Gil ; Iqbal, Zamin

United States: Nature Publishing Group

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