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PrimerHunter specifications


Unique identifier OMICS_03929
Name PrimerHunter
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PrimerHunter

PrimerHunter citations


Environmental DNA (eDNA) Detection Probability Is Influenced by Seasonal Activity of Organisms

PLoS One
PMCID: 5077074
PMID: 27776150
DOI: 10.1371/journal.pone.0165273

[…] Primers for N. alabamensis and S. depressus were designed using PrimerHunter [] and checked for cross-amplification with closely related taxa (). Due to the paucity of publicly available sequence data for both the focal Necturus and Sternotherus taxa, fragments fr […]


Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances

PMCID: 5053277
PMID: 27773942
DOI: 10.1111/1365-2664.12621

[…] the cytochrome c oxidase subunit 1 (COI) sequences for the 12 species of crayfishes likely to occur in lakes in the upper Midwest, USA (Peters et al. ; Table ), and subsequently designed primers with PrimerHunter (Duitama et al. ). Recommended primer pairs were synthesized by Integrated DNA Technologies (IDT) and evaluated in the laboratory for successful amplification with Orconectes rusticus DNA […]


Neuraminidase Subtyping of Avian Influenza Viruses with PrimerHunter Designed Primers and Quadruplicate Primer Pools

PLoS One
PMCID: 3843705
PMID: 24312367
DOI: 10.1371/journal.pone.0081842

[…] s reported in 2008 to subtype different NA subtypes []. Since 2009, several RT-PCR methods were reported for NA gene subtyping [-]. We have previously developed an open source software package called PrimerHunter for the design and selection of virus-subtyping primers. Different from the primer-design software employed by the above reports, PrimerHunter ensures the amplification specificity by acc […]


ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

Nucleic Acids Res
PMCID: 3241669
PMID: 21930509
DOI: 10.1093/nar/gkr732

[…] t adapted for long sequences (i.e. whole genomes) and do not take into account the taxonomic discrimination capacity of the amplified sequence during the primer selection process. More interestingly, PrimerHunter () was developed to select highly specific primers for distinguishing virus subtypes, a typical sensu lato barcoding application. Unfortunately, its efficiency on large data sets of long […]


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PrimerHunter institution(s)
Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA

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