Journal Article10.1021/acssynbio.1c00145
Sequence-Based Searching for SynBioHub Using VSEARCH.
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TL;DR: A new approach to scoring part similarity using SBOLExplorer is presented, which takes into account both the popularity and percentage match of parts.
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Abstract: 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.
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References
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
VSEARCH: a versatile open source tool for metagenomics
Torbjørn Rognes,Torbjørn Rognes,Tomas Flouri,Tomas Flouri,Ben Nichols,Christopher Quince,Christopher Quince,Frédéric Mahé +7 more
TL;DR: VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with US EARCH for paired-ends read merging and dereplication.
SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology.
James Alastair McLaughlin,Chris J. Myers,Zach Zundel,Goksel Misirli,Michael Zhang,Irina Dana Ofiteru,Angel Goñi-Moreno,Anil Wipat +7 more
TL;DR: The adoption and use of SynBioHub, a community-driven effort, has the potential to overcome the reproducibility challenge across laboratories by helping to address the current lack of information about published designs.