ArticleNucleic acids research2009
iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Identifying Universal Fish Biomarker Genes in Response to PCB126 Exposure by Comparative Transcriptomic Analyses.Current issues in molecular biology · 2024Article
- 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
- CODEHOP-Mediated PCR Improves HIV-1 Genotyping and Detection of Variants by MinION Sequencing.Microbiology spectrum · 2021Article
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- Five nuclear protein-coding markers for establishing a robust phylogenetic framework of niphargid crustaceans (Niphargidae: Amphipoda) and new molecular sequence data.Data in brief · 2019Article
- Molecular insight into the expression of metal transporter genes in Chryseobacterium sp. PMSZPI isolated from uranium deposit.PloS one · 2019Article
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- Novel Insights Into Bacterial Dimethylsulfoniopropionate Catabolism in the East China Sea.Frontiers in microbiology · 2018Article
- The feather-degrading bacterial community in two soils as revealed by a specific primer targeting serine-type keratinolytic proteases.World journal of microbiology & biotechnology · 2016Article
- Molecular Cloning and Characterization of Four Genes Encoding Ethylene Receptors Associated with Pineapple (Ananas comosus L.) Flowering.Frontiers in plant science · 2016Article
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- MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR.Nucleic acids research · 2015Article
- Cloning, expression, characterization and mutational analysis of the tfdA gene from Cupriavidus campinensis BJ71.World journal of microbiology & biotechnology · 2015Article
- Cloning of some heat shock proteins genes for further transcriptional study of Planktothrix agardhii exposed to abiotic stress.Folia microbiologica · 2015Article
- A systematic approach to novel virus discovery in emerging infectious disease outbreaks.The Journal of molecular diagnostics : JMD · 2015Review
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- Construction and characterization of VL-VH tail-parallel genetically engineered antibodies against staphylococcal enterotoxins.Immunologic research · 2015Article
- Pyrosequencing revealed SAR116 clade as dominant dddP-containing bacteria in oligotrophic NW Pacific Ocean.PloS one · 2015Article
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Authors and funding
3 authors.
Funding
Abstract
PCR amplification using COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOPs) has proven to be highly effective for identifying unknown pathogens and characterizing novel genes. We describe iCODEHOP; a new interactive web application that simplifies the process of designing and selecting CODEHOPs from multiply-aligned protein sequences. iCODEHOP intelligently guides the user through the degenerate primer design process including uploading sequences, creating a multiple alignment, deriving CODEHOPs and calculating their annealing temperatures. The user can quickly scan over an entire set of degenerate primers designed by the program to assess their relative quality and select individual primers for further analysis. The program displays phylogenetic information for input sequences and allows the user to easily design new primers from selected sequence sub-clades. It also allows the user to bias primer design to favor specific clades or sequences using sequence weights. iCODEHOP is freely available to all interested researchers at https://icodehop.cphi.washington.edu/i-codehop-context/Welcome.
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Registered trials
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