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HYDEN specifications

Information


Unique identifier OMICS_02338
Name HYDEN
Alternative name HighlY DEgeNerate primers
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publications for HighlY DEgeNerate primers

HYDEN citations

 (42)
library_books

Field validation of recombinant antigen immunoassays for diagnosis of Lassa fever

2018
Sci Rep
PMCID: 5897328
PMID: 29651117
DOI: 10.1038/s41598-018-24246-w

[…] ly published methods,. The Trombley qPCR assay targets the LASV glycoprotein gene with non-degenerate primers and probe. The Nikisins qPCR assay targets the LASV polymerase gene and utilizes a set of highly degenerate primers and probe. Clinical excess serum samples stored at −20 C were thawed at 4 C overnight. Viral RNA was extracted using QIAamp Viral RNA Mini Kit according to manufacturer’s ins […]

library_books

Production of eicosapentaenoic acid by application of a delta 6 desaturase with the highest ALA catalytic activity in algae

2018
Microb Cell Fact
PMCID: 5766975
PMID: 29331150
DOI: 10.1186/s12934-018-0857-3

[…] formation of FADS6 from Parietochloris incisa, Thalassiosira pseudonana Glossomastix chrysoplasta and Phaeodactylum tricornutum (GenBank accession nos. GU390532, AY817155, AAU11445 and AY082393), two highly degenerate primers (Additional file : Table S1) were designed to target sequences corresponding to the heme-binding motif of the cyt b5-like domain and the third His-rich motif in DsFADS6. The […]

library_books

DNA metabarcoding of littoral hard bottom communities: high diversity and database gaps revealed by two molecular markers

2018
PeerJ
PMCID: 5937484
PMID: 29740514
DOI: 10.7717/peerj.4705

[…] s procedures able to cope with the high degree of genetic diversity obtained. We think that the procedures presented here, which include extraction of DNA from separate size fractions, a novel set of highly degenerate primers for COI, and improved bioinformatics pipelines for data treatment, including new reference databases for eukaryotes, will help face the challenges related to metabarcoding of […]

library_books

Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding

2017
Sci Rep
PMCID: 5732254
PMID: 29247210
DOI: 10.1038/s41598-017-17333-x

[…] generacy and amplicon sequence conservation (Table , Figs  and , Suppl. Figure 2A). Significantly increased Simpson indexes and species richness were found for loci with high sequence conservation or highly degenerate primers (Pairwise Wilcoxon test, FDR corrected P < 0.05). A similar association was found for beta diversity. Jaccard distance and Bray Curtis dissimilarity between the actual specim […]

library_books

Performance of DNA metabarcoding, standard barcoding, and morphological approach in the identification of host–parasitoid interactions

2017
PLoS One
PMCID: 5728528
PMID: 29236697
DOI: 10.1371/journal.pone.0187803

[…] ing library preparation. We performed DNA extractions from mixed tissues following the same protocol as for standard barcoding (see above). To ensure broad recovery of taxa from mock samples, we used highly-degenerate primers for the amplification of COI markers: Fol-degen-for 5’-TCNACNAAYCAYAARRAYATYGG-3’ and Fol-degen-rev 5’-TANACYTCNGGRTGNCCRAARAAYCA-3’ []. A two-step PCR design was applied in […]

library_books

Immune Repertoire after Immunization As Seen by Next Generation Sequencing and Proteomics

2017
Front Immunol
PMCID: 5650670
PMID: 29085363
DOI: 10.3389/fimmu.2017.01286

[…] hFidelity buffer (New England Biolabs, Ipswich, MA, USA). The cDNA was amplified with a multiplex degenerate forward primer set and a common reverse primer. Forward PCR primers were designed with the HYDEN degenerate primer design tool () and are listed in the Supplementary Material. The PCR was run in a touchdown fashion for 26 cycles, each cycle reducing the annealing temperature by 0.5°C starti […]

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HYDEN institution(s)
School Of Computer Science, Tel-Aviv University, Ramat-Aviv, Tel-Aviv, Israel

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