{"id":"https://openalex.org/W2015616366","doi":"https://doi.org/10.1093/nar/gki394","title":"OrfPredictor: predicting protein-coding regions in EST-derived sequences","display_name":"OrfPredictor: predicting protein-coding regions in EST-derived sequences","publication_year":2005,"publication_date":"2005-06-26","ids":{"openalex":"https://openalex.org/W2015616366","doi":"https://doi.org/10.1093/nar/gki394","mag":"2015616366","pmid":"https://pubmed.ncbi.nlm.nih.gov/15980561"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki394","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W677/7622778/gki394.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":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W677/7622778/gki394.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042486252","display_name":"Xiang Jia Min","orcid":"https://orcid.org/0000-0001-7978-0596"},"institutions":[{"id":"https://openalex.org/I60158472","display_name":"Concordia University","ror":"https://ror.org/0420zvk78","country_code":"CA","type":"education","lineage":["https://openalex.org/I60158472"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"X. J. Min","raw_affiliation_strings":["Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada H4B 1R6"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada H4B 1R6","institution_ids":["https://openalex.org/I60158472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041471776","display_name":"Gregory Butler","orcid":"https://orcid.org/0000-0002-6938-0879"},"institutions":[{"id":"https://openalex.org/I4210151791","display_name":"Genomics (United Kingdom)","ror":"https://ror.org/053a6xa29","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151791"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"G. Butler","raw_affiliation_strings":["Centre for Structural and Functional Genomics,","Department of Computer Science and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Structural and Functional Genomics,","institution_ids":["https://openalex.org/I4210151791"]},{"raw_affiliation_string":"Department of Computer Science and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007709837","display_name":"Reginald Storms","orcid":null},"institutions":[{"id":"https://openalex.org/I4210151791","display_name":"Genomics (United Kingdom)","ror":"https://ror.org/053a6xa29","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151791"]},{"id":"https://openalex.org/I60158472","display_name":"Concordia University","ror":"https://ror.org/0420zvk78","country_code":"CA","type":"education","lineage":["https://openalex.org/I60158472"]}],"countries":["CA","GB"],"is_corresponding":false,"raw_author_name":"R. Storms","raw_affiliation_strings":["Centre for Structural and Functional Genomics,","Department of Biology, Concordia University, Montreal, Quebec, Canada H4B 1R6"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Structural and Functional Genomics,","institution_ids":["https://openalex.org/I4210151791"]},{"raw_affiliation_string":"Department of Biology, Concordia University, Montreal, Quebec, Canada H4B 1R6","institution_ids":["https://openalex.org/I60158472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060119095","display_name":"Adrian Tsang","orcid":"https://orcid.org/0000-0002-5892-4797"},"institutions":[{"id":"https://openalex.org/I4210151791","display_name":"Genomics (United Kingdom)","ror":"https://ror.org/053a6xa29","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151791"]},{"id":"https://openalex.org/I60158472","display_name":"Concordia University","ror":"https://ror.org/0420zvk78","country_code":"CA","type":"education","lineage":["https://openalex.org/I60158472"]}],"countries":["CA","GB"],"is_corresponding":false,"raw_author_name":"A. Tsang","raw_affiliation_strings":["Centre for Structural and Functional Genomics,","Department of Biology, Concordia University, Montreal, Quebec, Canada H4B 1R6"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Structural and Functional Genomics,","institution_ids":["https://openalex.org/I4210151791"]},{"raw_affiliation_string":"Department of Biology, Concordia University, Montreal, Quebec, Canada H4B 1R6","institution_ids":["https://openalex.org/I60158472"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5042486252"],"corresponding_institution_ids":["https://openalex.org/I60158472"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.2559,"has_fulltext":true,"cited_by_count":418,"citation_normalized_percentile":{"value":0.77311622,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"33","issue":"Web Server","first_page":"W677","last_page":"W680"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7709454298019409},{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.6395854949951172},{"id":"https://openalex.org/keywords/coding-region","display_name":"Coding region","score":0.5806328058242798},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5784193277359009},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.5416856408119202},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49304935336112976},{"id":"https://openalex.org/keywords/reading-frame","display_name":"Reading frame","score":0.4542132616043091},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4048589766025543},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.17511892318725586},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11746463179588318},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.06824779510498047}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7709454298019409},{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.6395854949951172},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.5806328058242798},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5784193277359009},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.5416856408119202},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49304935336112976},{"id":"https://openalex.org/C166253671","wikidata":"https://www.wikidata.org/wiki/Q923372","display_name":"Reading frame","level":5,"score":0.4542132616043091},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4048589766025543},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.17511892318725586},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11746463179588318},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.06824779510498047},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"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":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gki394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki394","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W677/7622778/gki394.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":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15980561","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15980561","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:10.1.1.104.5024","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.104.5024","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/cgi/screenpdf/33/suppl_2/W677.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:155182","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1160155","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gki394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki394","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W677/7622778/gki394.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":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.8799999952316284,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2015616366.pdf","grobid_xml":"https://content.openalex.org/works/W2015616366.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1993158258","https://openalex.org/W2004589024","https://openalex.org/W2022366078","https://openalex.org/W2055043387","https://openalex.org/W2094448442","https://openalex.org/W2144548050","https://openalex.org/W2161746138","https://openalex.org/W4236236547"],"related_works":["https://openalex.org/W2092940849","https://openalex.org/W2096622955","https://openalex.org/W4287110707","https://openalex.org/W2059202803","https://openalex.org/W2145417073","https://openalex.org/W2091615508","https://openalex.org/W1983767600","https://openalex.org/W1996672697","https://openalex.org/W2005844856","https://openalex.org/W2052050039"],"abstract_inverted_index":{"OrfPredictor":[0,92,104],"is":[1,59,105],"a":[2,20,69],"web":[3],"server":[4],"designed":[5],"for":[6,100],"identifying":[7],"protein-coding":[8],"regions":[9,29],"in":[10,22,37,64],"expressed":[11],"sequence":[12],"tag":[13],"(EST)-derived":[14],"sequences.":[15,56],"For":[16],"query":[17,55,75],"sequences":[18,63],"with":[19],"hit":[21],"BLASTX,":[23],"the":[24,27,32,43,50,54,60,65,74,77,82,86,94],"program":[25],"predicts":[26,42],"coding":[28,46,87],"based":[30,48],"on":[31,49],"translation":[33,78],"reading":[34,79],"frames":[35],"identified":[36],"BLASTX":[38],"alignments,":[39],"otherwise,":[40],"it":[41],"most":[44],"probable":[45],"region":[47,88],"intrinsic":[51],"signals":[52],"of":[53,96],"The":[57],"output":[58],"predicted":[61],"peptide":[62],"FASTA":[66],"format,":[67],"and":[68,81,90],"definition":[70],"line":[71],"that":[72],"includes":[73],"ID,":[76],"frame":[80],"nucleotide":[83],"positions":[84],"where":[85],"begins":[89],"ends.":[91],"facilitates":[93],"annotation":[95],"EST-derived":[97],"sequences,":[98],"particularly,":[99],"large-scale":[101],"EST":[102],"projects.":[103],"available":[106],"at":[107],"https://fungalgenome.concordia.ca/tools/OrfPredictor.html.":[108]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":18},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":38},{"year":2020,"cited_by_count":26},{"year":2019,"cited_by_count":31},{"year":2018,"cited_by_count":27},{"year":2017,"cited_by_count":32},{"year":2016,"cited_by_count":31},{"year":2015,"cited_by_count":41},{"year":2014,"cited_by_count":40},{"year":2013,"cited_by_count":30},{"year":2012,"cited_by_count":22}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
