Ultrafast search of all deposited bacterial and viral genomic data
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. Howeve...
| Main Authors: | , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Nature
2019
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| _version_ | 1797078904313217024 |
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| author | Bradley, P Den Bakker, H Rocha, E McVean, G Iqbal, Z |
| author_facet | Bradley, P Den Bakker, H Rocha, E McVean, G Iqbal, Z |
| author_sort | Bradley, P |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-07T00:38:10Z |
| format | Journal article |
| id | oxford-uuid:822271d1-e5f6-4397-950d-476b6836ccd4 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T00:38:10Z |
| publishDate | 2019 |
| publisher | Nature |
| record_format | dspace |
| spelling | oxford-uuid:822271d1-e5f6-4397-950d-476b6836ccd42022-03-26T21:35:11ZUltrafast search of all deposited bacterial and viral genomic dataJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:822271d1-e5f6-4397-950d-476b6836ccd4EnglishSymplectic Elements at OxfordNature2019Bradley, PDen Bakker, HRocha, EMcVean, GIqbal, ZExponentially 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. |
| spellingShingle | Bradley, P Den Bakker, H Rocha, E McVean, G Iqbal, Z Ultrafast search of all deposited bacterial and viral genomic data |
| title | Ultrafast search of all deposited bacterial and viral genomic data |
| title_full | Ultrafast search of all deposited bacterial and viral genomic data |
| title_fullStr | Ultrafast search of all deposited bacterial and viral genomic data |
| title_full_unstemmed | Ultrafast search of all deposited bacterial and viral genomic data |
| title_short | Ultrafast search of all deposited bacterial and viral genomic data |
| title_sort | ultrafast search of all deposited bacterial and viral genomic data |
| work_keys_str_mv | AT bradleyp ultrafastsearchofalldepositedbacterialandviralgenomicdata AT denbakkerh ultrafastsearchofalldepositedbacterialandviralgenomicdata AT rochae ultrafastsearchofalldepositedbacterialandviralgenomicdata AT mcveang ultrafastsearchofalldepositedbacterialandviralgenomicdata AT iqbalz ultrafastsearchofalldepositedbacterialandviralgenomicdata |