ArticleNucleic acids research2003
CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 papers.
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Who cites it
144 citing papers in PubMed.
- Surveillance of upper respiratory infections using a new multiplex PCR assay compared to conventional methods during the influenza season in Taiwan.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2017Trial
- Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets.BMC bioinformatics · 2025Article
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- Biochemical and Phylogenetic Analysis of ItalianPlants (Basel, Switzerland) · 2023Article
- Development of short-target primers for species identification in biological studies of Carnivora.Ecology and evolution · 2023Article
- Molecular Tools to Identify and Characterize Malignant Catarrhal Fever Viruses (MCFV) of Ruminants and CaptiveViruses · 2022Review
- An outbreak of human Rhinovirus-A21 infection in a psychiatric ward during COVID-19 pandemic.Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi · 2022Article
- A mechanistic study of the influence of nitrogen and energy availability on the NH4+ sensitivity of nitrogen assimilation in Synechococcus.Journal of experimental botany · 2022Article
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- rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses.BMC bioinformatics · 2022Article
- Antibodies targeting the European lobster (Palinurus elephas) vitellogenin developed by mRNA isolation and in-silico-designed antigenic peptides.Biology open · 2022Article
- CODEHOP-Mediated PCR Improves HIV-1 Genotyping and Detection of Variants by MinION Sequencing.Microbiology spectrum · 2021Article
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- Absence of Polyphenol Oxidase inPlants (Basel, Switzerland) · 2020Article
- Aerobic and oxygen-limited naphthalene-amended enrichments induced the dominance of Pseudomonas spp. from a groundwater bacterial biofilm.Applied microbiology and biotechnology · 2020Article
- Of Retinoids and Organotins: The Evolution of the Retinoid X Receptor in Metazoa.Biomolecules · 2020Article
- Bacteria are important dimethylsulfoniopropionate producers in coastal sediments.Nature microbiology · 2019Article
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- Discrimination ofExperimental and therapeutic medicine · 2019Article
84 more citing papers are in PubMed but not listed here.
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We have developed a new primer design strategy for PCR amplification of distantly related gene sequences based on consensus-degenerate hybrid oligonucleotide primers (CODEHOPs). An interactive program has been written to design CODEHOP PCR primers from conserved blocks of amino acids within multiply-aligned protein sequences. Each CODEHOP consists of a pool of related primers containing all possible nucleotide sequences encoding 3-4 highly conserved amino acids within a 3' degenerate core. A longer 5' non-degenerate clamp region contains the most probable nucleotide predicted for each flanking codon. CODEHOPs are used in PCR amplification to isolate distantly related sequences encoding the conserved amino acid sequence. The primer design software and the CODEHOP PCR strategy have been utilized for the identification and characterization of new gene orthologs and paralogs in different plant, animal and bacterial species. In addition, this approach has been successful in identifying new pathogen species. The CODEHOP designer (http://blocks.fhcrc.org/codehop.html) is linked to BlockMaker and the Multiple Alignment Processor within the Blocks Database World Wide Web (http://blocks.fhcrc.org).
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