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rCRUX Generated ITS2 Plants Reference Database

Authors: Zachary Gold; Emily Curd; Luna Gal; Ramon Gallego; Shaun Nielsen;

rCRUX Generated ITS2 Plants Reference Database

Abstract

rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: ITS2 Plants Gene: ITS2 Length of Target: 450-550 get_seeds_local() minimum length: 315 get_seeds_local() maximum length: 600 blast_seeds() minimum length: 270 blast_seeds() maximum length: 560 max_to_blast: 100 Forward Sequence (5'-3'): ATGCGATACTTGGTGTGAAT Reverse Sequence (5'-3'): GACGCTTCTCCAGACTACAAT Reference: Gu, W., Song, J., Cao, Y., Sun, Q., Yao, H., Wu, Q., ... & Duan, J. (2013). Application of the ITS2 region for barcoding medicinal plants of Selaginellaceae in Pteridophyta. PloS one, 8(6), e67818. https://doi.org/10.1371/journal.pone.0067818 We chose default rCRUX parameters for get_blast_seeds() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for blast_seeds() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.

Related Organizations
Keywords

Metabarcoding, eDNA, ITS, Plants, Reference barcode database, Plant ITS2, NOAA, CalCOFI, rCRUX

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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