{"id":"https://openalex.org/W2146351150","doi":"https://doi.org/10.1093/nar/gkg524","title":"CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design","display_name":"CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design","publication_year":2003,"publication_date":"2003-06-25","ids":{"openalex":"https://openalex.org/W2146351150","doi":"https://doi.org/10.1093/nar/gkg524","mag":"2146351150","pmid":"https://pubmed.ncbi.nlm.nih.gov/12824413"},"language":"es","primary_location":{"id":"doi:10.1093/nar/gkg524","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg524","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3763/9487165/gkg524.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/nar/article-pdf/31/13/3763/9487165/gkg524.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060027930","display_name":"Timothy M. Rose","orcid":"https://orcid.org/0000-0001-7646-0028"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"T. Rose","raw_affiliation_strings":["Department of Pathobiology, School of Public Health and Community Medicine, University of Washington, Seattle, WA 98195, USA. trose@u.washington.edu","Department of Pathobiology, School of Public Health and Community Medicine, University of Washington, Seattle, WA 98195, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pathobiology, School of Public Health and Community Medicine, University of Washington, Seattle, WA 98195, USA. trose@u.washington.edu","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Pathobiology, School of Public Health and Community Medicine, University of Washington, Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5060027930"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":4.3732,"has_fulltext":true,"cited_by_count":413,"citation_normalized_percentile":{"value":0.95129766,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"31","issue":"13","first_page":"3763","last_page":"3766"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10685","display_name":"Viral-associated cancers and disorders","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10685","display_name":"Viral-associated cancers and disorders","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10981","display_name":"Cytomegalovirus and herpesvirus research","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10625","display_name":"Herpesvirus Infections and Treatments","score":0.9865000247955322,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.9033913612365723},{"id":"https://openalex.org/keywords/primer","display_name":"Primer (cosmetics)","score":0.8190649747848511},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.7015361785888672},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6217021942138672},{"id":"https://openalex.org/keywords/oligonucleotide","display_name":"Oligonucleotide","score":0.5485728979110718},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.5369982123374939},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46615609526634216},{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.46248963475227356},{"id":"https://openalex.org/keywords/nucleic-acid-sequence","display_name":"Nucleic acid sequence","score":0.4609231948852539},{"id":"https://openalex.org/keywords/polymerase-chain-reaction","display_name":"Polymerase chain reaction","score":0.4434365928173065},{"id":"https://openalex.org/keywords/in-silico-pcr","display_name":"In silico PCR","score":0.4290728271007538},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.41755953431129456},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.33371397852897644},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.16208645701408386},{"id":"https://openalex.org/keywords/multiplex-polymerase-chain-reaction","display_name":"Multiplex polymerase chain reaction","score":0.09556138515472412}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9033913612365723},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.8190649747848511},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.7015361785888672},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6217021942138672},{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.5485728979110718},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.5369982123374939},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46615609526634216},{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.46248963475227356},{"id":"https://openalex.org/C84148353","wikidata":"https://www.wikidata.org/wiki/Q863908","display_name":"Nucleic acid sequence","level":3,"score":0.4609231948852539},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.4434365928173065},{"id":"https://openalex.org/C200658500","wikidata":"https://www.wikidata.org/wiki/Q4112082","display_name":"In silico PCR","level":5,"score":0.4290728271007538},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.41755953431129456},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.33371397852897644},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.16208645701408386},{"id":"https://openalex.org/C90583042","wikidata":"https://www.wikidata.org/wiki/Q1952456","display_name":"Multiplex polymerase chain reaction","level":4,"score":0.09556138515472412},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009841","descriptor_name":"Oligonucleotides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkg524","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg524","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3763/9487165/gkg524.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:12824413","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12824413","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.335.6350","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.335.6350","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/31/13/3763.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:158805","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC168931","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168931","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168931","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/168931","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkg524","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg524","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3763/9487165/gkg524.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.6299999952316284}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2146351150.pdf","grobid_xml":"https://content.openalex.org/works/W2146351150.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1970999032","https://openalex.org/W1991271048","https://openalex.org/W2041877620","https://openalex.org/W2052532932","https://openalex.org/W2117427088","https://openalex.org/W2125811524","https://openalex.org/W2127798439","https://openalex.org/W2155850509","https://openalex.org/W2156628505","https://openalex.org/W4229946422","https://openalex.org/W4309958857"],"related_works":["https://openalex.org/W2181549235","https://openalex.org/W1973727281","https://openalex.org/W2046212479","https://openalex.org/W3209520725","https://openalex.org/W2003319012","https://openalex.org/W2031006065","https://openalex.org/W2514476306","https://openalex.org/W2023479323","https://openalex.org/W2143582965","https://openalex.org/W2044507120"],"abstract_inverted_index":{"We":[0],"have":[1,111],"developed":[2],"a":[3,48,65],"new":[4,120,141],"primer":[5,103],"design":[6,30,104],"strategy":[7,110],"for":[8,81,114],"PCR":[9,32,89,109],"amplification":[10,90],"of":[11,37,47,50,119],"distantly":[12,93],"related":[13,51,94],"gene":[14,121],"sequences":[15,57,95],"based":[16],"on":[17],"consensus-degenerate":[18],"hybrid":[19],"oligonucleotide":[20],"primers":[21,33,52],"(CODEHOPs).":[22],"An":[23],"interactive":[24],"program":[25],"has":[26,136],"been":[27,112,137],"written":[28],"to":[29,91,150],"CODEHOP":[31,45,108,145],"from":[34],"conserved":[35,61,98],"blocks":[36],"amino":[38,62,99],"acids":[39,63],"within":[40,64,157],"multiply-aligned":[41],"protein":[42],"sequences.":[43],"Each":[44],"consists":[46],"pool":[49],"containing":[53],"all":[54],"possible":[55],"nucleotide":[56,79],"encoding":[58,96],"3-4":[59],"highly":[60],"3'":[66],"degenerate":[67],"core.":[68],"A":[69],"longer":[70],"5'":[71],"non-degenerate":[72],"clamp":[73],"region":[74],"contains":[75],"the":[76,97,107,115,153,158],"most":[77],"probable":[78],"predicted":[80],"each":[82],"flanking":[83],"codon.":[84],"CODEHOPs":[85],"are":[86],"used":[87],"in":[88,125,139],"isolate":[92],"acid":[100],"sequence.":[101],"The":[102,144],"software":[105],"and":[106,117,123,129,152],"utilized":[113],"identification":[116],"characterization":[118],"orthologs":[122],"paralogs":[124],"different":[126],"plant,":[127],"animal":[128],"bacterial":[130],"species.":[131,143],"In":[132],"addition,":[133],"this":[134],"approach":[135],"successful":[138],"identifying":[140],"pathogen":[142],"designer":[146],"(http://blocks.fhcrc.org/codehop.html)":[147],"is":[148],"linked":[149],"BlockMaker":[151],"Multiple":[154],"Alignment":[155],"Processor":[156],"Blocks":[159],"Database":[160],"World":[161],"Wide":[162],"Web":[163],"(http://blocks.fhcrc.org).":[164]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":14},{"year":2018,"cited_by_count":15},{"year":2017,"cited_by_count":16},{"year":2016,"cited_by_count":19},{"year":2015,"cited_by_count":23},{"year":2014,"cited_by_count":27},{"year":2013,"cited_by_count":39},{"year":2012,"cited_by_count":42}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}