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Fast Search of Thousands of Short-Read Sequencing Experiments
We introduce Sequence Bloom Trees, a method for querying thousands of short-read sequencing experiments by sequence 485 times faster than existing approaches. The approach searches large data archives for all experiments that involve a given sequence. We use Sequence Bloom Trees to search 2652 human...
| Autores principales: | , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
2016
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804353/ https://www.ncbi.nlm.nih.gov/pubmed/26854477 http://dx.doi.org/10.1038/nbt.3442 |
| _version_ | 1782423007908593664 |
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| author | Solomon, Brad Kingsford, Carl |
| author_facet | Solomon, Brad Kingsford, Carl |
| author_sort | Solomon, Brad |
| collection | PubMed |
| description | We introduce Sequence Bloom Trees, a method for querying thousands of short-read sequencing experiments by sequence 485 times faster than existing approaches. The approach searches large data archives for all experiments that involve a given sequence. We use Sequence Bloom Trees to search 2652 human blood, breast, and brain RNA-seq experiments for all 214,293 known transcripts in under 4 days using less than 239 MB of RAM and a single CPU. |
| format | Online Article Text |
| id | pubmed-4804353 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2016 |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-48043532016-08-08 Fast Search of Thousands of Short-Read Sequencing Experiments Solomon, Brad Kingsford, Carl Nat Biotechnol Article We introduce Sequence Bloom Trees, a method for querying thousands of short-read sequencing experiments by sequence 485 times faster than existing approaches. The approach searches large data archives for all experiments that involve a given sequence. We use Sequence Bloom Trees to search 2652 human blood, breast, and brain RNA-seq experiments for all 214,293 known transcripts in under 4 days using less than 239 MB of RAM and a single CPU. 2016-02-08 2016-03 /pmc/articles/PMC4804353/ /pubmed/26854477 http://dx.doi.org/10.1038/nbt.3442 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms |
| spellingShingle | Article Solomon, Brad Kingsford, Carl Fast Search of Thousands of Short-Read Sequencing Experiments |
| title | Fast Search of Thousands of Short-Read Sequencing Experiments |
| title_full | Fast Search of Thousands of Short-Read Sequencing Experiments |
| title_fullStr | Fast Search of Thousands of Short-Read Sequencing Experiments |
| title_full_unstemmed | Fast Search of Thousands of Short-Read Sequencing Experiments |
| title_short | Fast Search of Thousands of Short-Read Sequencing Experiments |
| title_sort | fast search of thousands of short-read sequencing experiments |
| topic | Article |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804353/ https://www.ncbi.nlm.nih.gov/pubmed/26854477 http://dx.doi.org/10.1038/nbt.3442 |
| work_keys_str_mv | AT solomonbrad fastsearchofthousandsofshortreadsequencingexperiments AT kingsfordcarl fastsearchofthousandsofshortreadsequencingexperiments |