rCRUX Generated MiSebastes Reference Database

rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: MiSebastes Gene: CytB Length of Target: 153 get_seeds_local() minimum length: 107 get_seeds_local() maximum length: 199 blast_seeds() minimum length: 71 blast_seeds() maximum length: 163 max_to_blast: 100 Forward Sequence (5'-3'): AAGCTCATTCAAGTGCTT Reverse Sequence (5'-3'): GACCACTTACACAATTCT Reference: Min, M. A., Barber, P. H., & Gold, Z. (2021). MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes). Conservation Genetics Resources, 13(4), 447-456. https://doi.org/10.1007/s12686-021-01219-2 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

Autonomous University of Madrid
Spain
Landmark College
United States

Keywords

Sebastes, Metabarcoding, eDNA, Reference barcode database, NOAA, Rockfish, rCRUX, CalCOFI

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