Sequence-Based Searching for SynBioHub Using VSEARCH

doi:10.1021/acssynbio.1c00145

2022-01-21

PRE

Eric Yu

Jeanet Mante

Chris J. Myers *

DOI：10.1021/acssynbio.1c00145

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摘要

En 中文

The ability to search for a part by its sequence is crucial for a large repository of parts. Prior to this work, however, this was not possible on SynBioHub. Sequence-based search is now integrated into SynBioHub, allowing users to find a part by a sequence provided in plain text or a supported file format. This sequence-based search feature is accessible to users via SynBioHub's web interface, or programmatically through its API. The core implementation of the tool uses VSEARCH, an open source, global alignment search tool, and it is integrated into SBOLExplorer, an open source distributed search engine used by SynBioHub. We present a new approach to scoring part similarity using SBOLExplorer, which takes into account both the popularity and percentage match of parts.

Keyword:

SBOL

VSEARCH

USEARCH

SynBioHub

SBOLExplorer

PageRank

期刊

ACS Synthetic Biology

IF:

3.9

论文数:

3.9K

被引数:

1.2W

机构

University of Utah

学者数:

3.0W

论文数: 2.2W

被引数: 4.6W

Utah System of Higher Education

学者数:

4.6W

论文数: 4.0W

被引数: 161

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