完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.author | Chang, Chia-Hua | en_US |
dc.contributor.author | Chou, Min-Te | en_US |
dc.contributor.author | Wu, Yi-Chung | en_US |
dc.contributor.author | Hong, Ting-Wei | en_US |
dc.contributor.author | Li, Yun-Lung | en_US |
dc.contributor.author | Yang, Chia-Hsiang | en_US |
dc.contributor.author | Hung, Jui-Hung | en_US |
dc.date.accessioned | 2017-04-21T06:56:39Z | - |
dc.date.available | 2017-04-21T06:56:39Z | - |
dc.date.issued | 2016-11-15 | en_US |
dc.identifier.issn | 1367-4803 | en_US |
dc.identifier.uri | http://dx.doi.org/10.1093/bioinformatics/btw419 | en_US |
dc.identifier.uri | http://hdl.handle.net/11536/133094 | - |
dc.description.abstract | Motivation: The Full-text index in Minute space (FM-index) derived from the Burrows-Wheeler transform (BWT) is broadly used for fast string matching in large genomes or a huge set of sequencing reads. Several graphic processing unit (GPU) accelerated aligners based on the FM-index have been proposed recently; however, the construction of the index is still handled by central processing unit (CPU), only parallelized in data level (e.g. by performing block-wise suffix sorting in GPU), or not scalable for large genomes. Results: To fulfill the need for a more practical, hardware-parallelizable indexing and matching approach, we herein propose sBWT based on a BWT variant (i.e. Schindler transform) that can be built with highly simplified hardware-acceleration-friendly algorithms and still suffices accurate and fast string matching in repetitive references. In our tests, the implementation achieves significant speedups in indexing and searching compared with other BWT-based tools and can be applied to a variety of domains. | en_US |
dc.language.iso | en_US | en_US |
dc.title | sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping | en_US |
dc.identifier.doi | 10.1093/bioinformatics/btw419 | en_US |
dc.identifier.journal | BIOINFORMATICS | en_US |
dc.citation.volume | 32 | en_US |
dc.citation.issue | 22 | en_US |
dc.citation.spage | 3498 | en_US |
dc.citation.epage | 3500 | en_US |
dc.contributor.department | 生物科技學系 | zh_TW |
dc.contributor.department | 生物資訊及系統生物研究所 | zh_TW |
dc.contributor.department | 分子醫學與生物工程研究所 | zh_TW |
dc.contributor.department | Department of Biological Science and Technology | en_US |
dc.contributor.department | Institude of Bioinformatics and Systems Biology | en_US |
dc.contributor.department | Institute of Molecular Medicine and Bioengineering | en_US |
dc.identifier.wosnumber | WOS:000392748700019 | en_US |
顯示於類別: | 期刊論文 |