cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7965978
title: Internet-delivered cognitive behavioural therapy programme to reduce depressive symptoms in patients with multiple sclerosis: a multicentre, randomised, controlled, phase 3 trial in Germany and the USA

description: Patient-level data on primary and secondary endpoints of an international multicenter randomized controlled trial of internet-delivered cognitive behavioral therapy (iCBT) to reduce depressive symptoms in multiple sclerosis (MS). ClinicalTrials.gov Identifier: NCT02740361
DOI: 10.5281/zenodo.7965979
title: Internet-delivered cognitive behavioural therapy programme to reduce depressive symptoms in patients with multiple sclerosis: a multicentre, randomised, controlled, phase 3 trial in Germany and the USA

description: Patient-level data on primary and secondary endpoints of an international multicenter randomized controlled trial of internet-delivered cognitive behavioral therapy (iCBT) to reduce depressive symptoms in multiple sclerosis (MS). ClinicalTrials.gov Identifier: NCT02740361
DOI: 10.25345/c5jw86z3z
title: MassIVE MSV000093045 - Eva and Anil first test - polymer contaminations
title: Non-target metabolomics of environmental samples using Methanol extraction.
DOI: 10.5281/zenodo.8409199
title: rCRUX Generated Cephalpod 18S Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Ceph18S<br> Gene: 18S<br> Length of Target: 150–190<br> get_seeds_local() minimum length: 105<br> get_seeds_local() maximum length: 235<br> blast_seeds() minimum length: 65<br> blast_seeds() maximum length: 195<br> max_to_blast: 100<br> Forward Sequence (5'-3'): CGCGGCGCTACATATTAGAC<br> Reverse Sequence (5'-3'): GCACTTAACCGACCGTCGAC<br> Reference: D. S. W. de Jonge, V. Merten, T. Bayer, O. Puebla, T. B. H. Reusch, H.-J. T. Hoving, A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region. R. Soc. Open Sci. 8, 201388 (2021) https://doi.org/10.1098/rsos.201388 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909639
title: rCRUX Generated Cephalpod 18S Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Ceph18S<br> Gene: 18S<br> Length of Target: 150–190<br> get_seeds_local() minimum length: 105<br> get_seeds_local() maximum length: 235<br> blast_seeds() minimum length: 65<br> blast_seeds() maximum length: 195<br> max_to_blast: 100<br> Forward Sequence (5'-3'): CGCGGCGCTACATATTAGAC<br> Reverse Sequence (5'-3'): GCACTTAACCGACCGTCGAC<br> Reference: D. S. W. de Jonge, V. Merten, T. Bayer, O. Puebla, T. B. H. Reusch, H.-J. T. Hoving, A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region. R. Soc. Open Sci. 8, 201388 (2021) https://doi.org/10.1098/rsos.201388 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8409202
title: rCRUX Generated MiFish Universal 12S Expanded Reference Database

description: rCRUX generated reference database using NCBI nt blast database and an additional custom blast database comprised of all Actinopterygii mitogenomes. Both blast databases were downloaded in December 2022. Primer Name: MiFish Universal<br> Gene: 12S<br> Length of Target: 163–185<br> get_seeds_local() minimum length: 170<br> get_seeds_local() maximum length: 250<br> blast_seeds() minimum length: 140<br> blast_seeds() maximum length: 250<br> max_to_blast: 1000<br> Forward Sequence (5'-3'): GTGTCGGTAAAACTCGTGCCAGC<br> Reverse Sequence (5'-3'): CATAGTGGGGTATCTAATCCCAGTTTG<br> Reference: Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., ... & Kondoh, M. (2015). MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society open science, 2(7), 150088. https://doi.org/10.1098/rsos.150088 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7908864
title: rCRUX Generated MiFish Universal 12S Expanded Reference Database

description: rCRUX generated reference database using NCBI nt blast database and an additional custom blast database comprised of all Actinopterygii mitogenomes. Both blast databases were downloaded in December 2022. Primer Name: MiFish Universal<br> Gene: 12S<br> Length of Target: 163–185<br> get_seeds_local() minimum length: 170<br> get_seeds_local() maximum length: 250<br> blast_seeds() minimum length: 140<br> blast_seeds() maximum length: 250<br> max_to_blast: 1000<br> Forward Sequence (5'-3'): GTGTCGGTAAAACTCGTGCCAGC<br> Reverse Sequence (5'-3'): CATAGTGGGGTATCTAATCCCAGTTTG<br> Reference: Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., ... & Kondoh, M. (2015). MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society open science, 2(7), 150088. https://doi.org/10.1098/rsos.150088 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8409174
title: rCRUX Generated MarVer3 Marine Mammal Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: MarVer3 Marine Mammal<br> Gene: 16S<br> Length of Target: 232-274<br> get_seeds_local() minimum length: 160<br> get_seeds_local() maximum length: 345<br> blast_seeds() minimum length: 124<br> blast_seeds() maximum length: 309<br> max_to_blast: 100<br> Forward Sequence (5'-3'): AGACGAGAAGACCCTRTG<br> Reverse Sequence (5'-3'): GGATTGCGCTGTTATCCC<br> Reference: Valsecchi, E., Bylemans, J., Goodman, S. J., Lombardi, R., Carr, I., Castellano, L., ... & Galli, P. (2020). Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates. Environmental DNA, 2(4), 460-476. https://doi.org/10.1002/edn3.72 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909663
title: rCRUX Generated MarVer3 Marine Mammal Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: MarVer3 Marine Mammal<br> Gene: 16S<br> Length of Target: 232-274<br> get_seeds_local() minimum length: 160<br> get_seeds_local() maximum length: 345<br> blast_seeds() minimum length: 124<br> blast_seeds() maximum length: 309<br> max_to_blast: 100<br> Forward Sequence (5'-3'): AGACGAGAAGACCCTRTG<br> Reverse Sequence (5'-3'): GGATTGCGCTGTTATCCC<br> Reference: Valsecchi, E., Bylemans, J., Goodman, S. J., Lombardi, R., Carr, I., Castellano, L., ... & Galli, P. (2020). Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates. Environmental DNA, 2(4), 460-476. https://doi.org/10.1002/edn3.72 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8409176
title: rCRUX Generated Kelly Metazoan 16S Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Kelly Metazoan 16S<br> Gene: 16S<br> Length of Target: 114-160<br> get_seeds_local() minimum length: 80<br> get_seeds_local() maximum length: 195<br> blast_seeds() minimum length: 50<br> blast_seeds() maximum length: 168<br> max_to_blast: 100<br> Forward Sequence (5'-3'): AGTTACYYTAGGGATAACAGCG<br> Reverse Sequence (5'-3'): CCGGTCTGAACTCAGATCAYGT<br> Reference: Kelly, R. P., O’Donnell, J. L., Lowell, N. C., Shelton, A. O., Samhouri, J. F., Hennessey, S. M., ... & Williams, G. D. (2016). Genetic signatures of ecological diversity along an urbanization gradient. PeerJ, 4, e2444. https://doi.org/10.7717/peerj.2444 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909659
title: rCRUX Generated Kelly Metazoan 16S Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Kelly Metazoan 16S<br> Gene: 16S<br> Length of Target: 114-160<br> get_seeds_local() minimum length: 80<br> get_seeds_local() maximum length: 195<br> blast_seeds() minimum length: 50<br> blast_seeds() maximum length: 168<br> max_to_blast: 100<br> Forward Sequence (5'-3'): AGTTACYYTAGGGATAACAGCG<br> Reverse Sequence (5'-3'): CCGGTCTGAACTCAGATCAYGT<br> Reference: Kelly, R. P., O’Donnell, J. L., Lowell, N. C., Shelton, A. O., Samhouri, J. F., Hennessey, S. M., ... & Williams, G. D. (2016). Genetic signatures of ecological diversity along an urbanization gradient. PeerJ, 4, e2444. https://doi.org/10.7717/peerj.2444 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8409179
title: rCRUX Generated MiDeca Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: MiDeca<br> Gene: 16S<br> Length of Target: 154-184<br> get_seeds_local() minimum length: 105<br> get_seeds_local() maximum length: 230<br> blast_seeds() minimum length: 66<br> blast_seeds() maximum length: 191<br> max_to_blast: 50<br> Forward Sequence (5'-3'): GGACGATAAGACCCTATAAA<br> Reverse Sequence (5'-3'): ACGCTGTTATCCCTAAAGT<br> Reference: Komai, T., Gotoh, R.O., Sado, T. and Miya, M., 2019. Development of a new set of PCR primers for eDNA metabarcoding decapod crustaceans. Metabarcoding and Metagenomics, 3, p.e33835. https://doi.org/10.3897/mbmg.6.76534 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909669
title: rCRUX Generated MiDeca Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: MiDeca<br> Gene: 16S<br> Length of Target: 154-184<br> get_seeds_local() minimum length: 105<br> get_seeds_local() maximum length: 230<br> blast_seeds() minimum length: 66<br> blast_seeds() maximum length: 191<br> max_to_blast: 50<br> Forward Sequence (5'-3'): GGACGATAAGACCCTATAAA<br> Reverse Sequence (5'-3'): ACGCTGTTATCCCTAAAGT<br> Reference: Komai, T., Gotoh, R.O., Sado, T. and Miya, M., 2019. Development of a new set of PCR primers for eDNA metabarcoding decapod crustaceans. Metabarcoding and Metagenomics, 3, p.e33835. https://doi.org/10.3897/mbmg.6.76534 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8409184
title: rCRUX Generated ITS2 Plants Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: ITS2 Plants<br> Gene: ITS2<br> Length of Target: 450-550<br> get_seeds_local() minimum length: 315<br> get_seeds_local() maximum length: 600<br> blast_seeds() minimum length: 270<br> blast_seeds() maximum length: 560<br> max_to_blast: 100<br> Forward Sequence (5'-3'): ATGCGATACTTGGTGTGAAT<br> Reverse Sequence (5'-3'): GACGCTTCTCCAGACTACAAT<br> 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 <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909655
title: rCRUX Generated ITS2 Plants Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: ITS2 Plants<br> Gene: ITS2<br> Length of Target: 450-550<br> get_seeds_local() minimum length: 315<br> get_seeds_local() maximum length: 600<br> blast_seeds() minimum length: 270<br> blast_seeds() maximum length: 560<br> max_to_blast: 100<br> Forward Sequence (5'-3'): ATGCGATACTTGGTGTGAAT<br> Reverse Sequence (5'-3'): GACGCTTCTCCAGACTACAAT<br> 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 <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8409191
title: rCRUX Generated Fungal ITS Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Fungal_ITS gITS7/ITS4<br> Gene: FITS<br> Length of Target: 150-330<br> get_seeds_local() minimum length: 105<br> get_seeds_local() maximum length: 500<br> blast_seeds() minimum length: 65<br> blast_seeds() maximum length: 461<br> max_to_blast: 100<br> Forward Sequence (5'-3'): GTGARTCATCGARTCTTTG<br> Reverse Sequence (5'-3'): TCCTCCGCTTATTGATATGC<br> Reference: White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications, 18(1), 315–322.<br> Ihrmark, K., Bödeker, I., Cruz-Martinez, K., Friberg, H., Kubartova, A., Schenck, J., Strid, Y., Stenlid, J., Brandström-Durling, M., & Clemmensen, K. E. (2012). New primers to amplify the fungal ITS2 region–evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiology Ecology, 82(3), 666–677. https://doi.org/10.1111/j.1574-6941.2012.01437.x We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909648
title: rCRUX Generated Fungal ITS Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Fungal_ITS gITS7/ITS4<br> Gene: FITS<br> Length of Target: 150-330<br> get_seeds_local() minimum length: 105<br> get_seeds_local() maximum length: 500<br> blast_seeds() minimum length: 65<br> blast_seeds() maximum length: 461<br> max_to_blast: 100<br> Forward Sequence (5'-3'): GTGARTCATCGARTCTTTG<br> Reverse Sequence (5'-3'): TCCTCCGCTTATTGATATGC<br> Reference: White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications, 18(1), 315–322.<br> Ihrmark, K., Bödeker, I., Cruz-Martinez, K., Friberg, H., Kubartova, A., Schenck, J., Strid, Y., Stenlid, J., Brandström-Durling, M., & Clemmensen, K. E. (2012). New primers to amplify the fungal ITS2 region–evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiology Ecology, 82(3), 666–677. https://doi.org/10.1111/j.1574-6941.2012.01437.x We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8409198
title: rCRUX Generated Ford Fish 16S Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Ford Fish 16S<br> Gene: 16S<br> Length of Target: 330<br> get_seeds_local() minimum length: 279<br> get_seeds_local() maximum length: 477<br> blast_seeds() minimum length: 231<br> blast_seeds() maximum length: 429<br> max_to_blast: 1000<br> Forward Sequence (5'-3'): GCAATCACTTGTCTTTTAAATGAAGACC, GTAATCACTTGTCTTTTAAATGAAGACC<br> Reverse Sequence (5'-3'): GGATTGCGCTGTTATCCCTA<br> 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 <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909642
title: rCRUX Generated Ford Fish 16S Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Ford Fish 16S<br> Gene: 16S<br> Length of Target: 330<br> get_seeds_local() minimum length: 279<br> get_seeds_local() maximum length: 477<br> blast_seeds() minimum length: 231<br> blast_seeds() maximum length: 429<br> max_to_blast: 1000<br> Forward Sequence (5'-3'): GCAATCACTTGTCTTTTAAATGAAGACC, GTAATCACTTGTCTTTTAAATGAAGACC<br> Reverse Sequence (5'-3'): GGATTGCGCTGTTATCCCTA<br> 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 <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8409157
title: rCRUX Generated Teleo Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: teleo L1848/H1913<br> Gene: 12S<br> Length of Target: 100<br> get_seeds_local() minimum length: 70<br> get_seeds_local() maximum length: 130<br> blast_seeds() minimum length: 40<br> blast_seeds() maximum length: 100<br> max_to_blast: 100<br> Forward Sequence (5'-3'): ACACCGCCCGTCACTCT<br> Reverse Sequence (5'-3'): CTTCCGGTACACTTACCATG<br> Reference: Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., ... & Gaboriaud, C. (2016). Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929-942. https://doi.org/10.1111/mec.13428 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.7909697
title: rCRUX Generated Teleo Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: teleo L1848/H1913<br> Gene: 12S<br> Length of Target: 100<br> get_seeds_local() minimum length: 70<br> get_seeds_local() maximum length: 130<br> blast_seeds() minimum length: 40<br> blast_seeds() maximum length: 100<br> max_to_blast: 100<br> Forward Sequence (5'-3'): ACACCGCCCGTCACTCT<br> Reverse Sequence (5'-3'): CTTCCGGTACACTTACCATG<br> Reference: Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., ... & Gaboriaud, C. (2016). Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929-942. https://doi.org/10.1111/mec.13428 We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.
DOI: 10.5281/zenodo.8409160
title: rCRUX Generated Taberlet c/h trnl Reference Database

description: rCRUX generated reference database using NCBI nt blast database downloaded in December 2022. Primer Name: Taberlet c/h trnl<br> Gene: trnl<br> Length of Target: 150<br> get_seeds_local() minimum length: 105<br> get_seeds_local() maximum length: 150<br> blast_seeds() minimum length: 85<br> blast_seeds() maximum length: 128<br> max_to_blast: 100<br> Forward Sequence (5'-3'): CGAAATCGGTAGACGCTACG<br> Reverse Sequence (5'-3'): CCATTGAGTCTCTGCACCTATC<br> Reference: Taberlet, P., Gielly, L., Pautou, G., & Bouvet, J. (1991). Universal primers for amplification of three non-coding regions of. Plant molecular biology, 17, 1105-1109. & Taberlet, Pierre, Eric Coissac, François Pompanon, Ludovic Gielly, Christian Miquel, Alice Valentini, Thierry Vermat, Gerard Corthier, Christian Brochmann, and Eske Willerslev. "Power and limitations of the chloroplast trn L (UAA) intron for plant DNA barcoding." Nucleic acids research 35, no. 3 (2007): e14-e14. We chose default rCRUX parameters for <em>get_blast_seeds</em>() of percent coverage of 70, percent identity of 70, evalue 3e+7, and max number of blast alignments = '100000000' and for <em>blast_seeds</em>() of coverage of 70, percent identity of 70, evalue 3e+7, rank of genus, and max number of blast alignments = '10000000'.