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ELM: enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset
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| Title: | ELM: enhanced lowest common ancestor based method for detecting a pathogenic virus from a large sequence dataset |
| Authors: | Ueno, Keisuke Browse this author →KAKEN DB | | Ishii, Akihiro Browse this author →KAKEN DB | | Ito, Kimihito Browse this author →KAKEN DB |
| Keywords: | Next generation sequencing | | Virus discovery | | Diagnostic virology | | Virome | | Taxonomic identification |
| Issue Date: | 28-Jul-2014 |
| Publisher: | Biomed Central |
| Journal Title: | BMC Bioinformatics |
| Volume: | 15 |
| Start Page: | 254 |
| Publisher DOI: | 10.1186/1471-2105-15-254 |
| Abstract: | Background: Emerging viral diseases, most of which are caused by the transmission of viruses from animals to humans, pose a threat to public health. Discovering pathogenic viruses through surveillance is the key to preparedness for this potential threat. Next generation sequencing (NGS) helps us to identify viruses without the design of a specific PCR primer. The major task in NGS data analysis is taxonomic identification for vast numbers of sequences. However, taxonomic identification via a BLAST search against all the known sequences is a computational bottleneck. Description: Here we propose an enhanced lowest-common-ancestor based method (ELM) to effectively identify viruses from massive sequence data. To reduce the computational cost, ELM uses a customized database composed only of viral sequences for the BLAST search. At the same time, ELM adopts a novel criterion to suppress the rise in false positive assignments caused by the small database. As a result, identification by ELM is more than 1,000 times faster than the conventional methods without loss of accuracy. Conclusions: We anticipate that ELM will contribute to direct diagnosis of viral infections. |
| Rights: | http://creativecommons.org/licenses/by/2.0/ |
| Type: | article |
| URI: | http://hdl.handle.net/2115/57018 |
| Appears in Collections: | 人獣共通感染症国際共同研究所 (International Institute for Zoonosis Control) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
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Submitter: 伊藤 公人
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