rCRUX Generated Ford Fish 16S Reference Database
- 1. NOAA PMEL
- 2. Vermont Biomedical Research Network
- 3. Landmark College
- 4. Universidad Autónoma de Madrid
Description
rCRUX generated reference database using NCBI nt blast database downloaded in December 2022.
Primer Name: Ford Fish 16S
Gene: 16S
Length of Target: 330
get_seeds_local() minimum length: 279
get_seeds_local() maximum length: 477
blast_seeds() minimum length: 231
blast_seeds() maximum length: 429
max_to_blast: 1000
Forward Sequence (5'-3'): GCAATCACTTGTCTTTTAAATGAAGACC, GTAATCACTTGTCTTTTAAATGAAGACC
Reverse Sequence (5'-3'): GGATTGCGCTGTTATCCCTA
Reference: Ford MJ, Hempelmann J, Hanson MB, Ayres KL, Baird RW, et al. (2016) Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces. PLOS ONE 11(1): e0144956. https://doi.org/10.1371/journal.pone.0144956
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'.
Files
Files
(230.1 MB)
Name | Size | Download all |
---|---|---|
md5:e5608446cb1715b2e58f54a02ca0740f
|
230.1 MB | Download |