{"id":"https://openalex.org/W1999763852","doi":"https://doi.org/10.1093/bioinformatics/bti075","title":"ESTminer: a suite of programs for gene and allele identification","display_name":"ESTminer: a suite of programs for gene and allele identification","publication_year":2004,"publication_date":"2004-11-05","ids":{"openalex":"https://openalex.org/W1999763852","doi":"https://doi.org/10.1093/bioinformatics/bti075","mag":"1999763852","pmid":"https://pubmed.ncbi.nlm.nih.gov/15531616"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti075","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti075","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/5/691/48962529/bioinformatics_21_5_691.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","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/bioinformatics/article-pdf/21/5/691/48962529/bioinformatics_21_5_691.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089638887","display_name":"Rex T. Nelson","orcid":"https://orcid.org/0000-0001-6222-3347"},"institutions":[{"id":"https://openalex.org/I1312222531","display_name":"Agricultural Research Service","ror":"https://ror.org/02d2m2044","country_code":"US","type":"government","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rex T. Nelson","raw_affiliation_strings":["USDA-ARS, CICGR Ames, IA, USA","USDA-ARS, CICGR Ames, IA, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"USDA-ARS, CICGR Ames, IA, USA","institution_ids":["https://openalex.org/I1312222531"]},{"raw_affiliation_string":"USDA-ARS, CICGR Ames, IA, USA#TAB#","institution_ids":["https://openalex.org/I1312222531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041496985","display_name":"David Grant","orcid":"https://orcid.org/0000-0002-4611-6848"},"institutions":[{"id":"https://openalex.org/I1312222531","display_name":"Agricultural Research Service","ror":"https://ror.org/02d2m2044","country_code":"US","type":"government","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Grant","raw_affiliation_strings":["USDA-ARS, CICGR Ames, IA, USA","USDA-ARS, CICGR Ames, IA, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"USDA-ARS, CICGR Ames, IA, USA","institution_ids":["https://openalex.org/I1312222531"]},{"raw_affiliation_string":"USDA-ARS, CICGR Ames, IA, USA#TAB#","institution_ids":["https://openalex.org/I1312222531"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103567863","display_name":"Randy C. Shoemaker","orcid":null},"institutions":[{"id":"https://openalex.org/I1312222531","display_name":"Agricultural Research Service","ror":"https://ror.org/02d2m2044","country_code":"US","type":"government","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Randy C. Shoemaker","raw_affiliation_strings":["USDA-ARS, CICGR Ames, IA, USA","USDA-ARS, CICGR Ames, IA, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"USDA-ARS, CICGR Ames, IA, USA","institution_ids":["https://openalex.org/I1312222531"]},{"raw_affiliation_string":"USDA-ARS, CICGR Ames, IA, USA#TAB#","institution_ids":["https://openalex.org/I1312222531"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5089638887"],"corresponding_institution_ids":["https://openalex.org/I1312222531"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.8562,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.73615806,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"21","issue":"5","first_page":"691","last_page":"693"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.2476000040769577,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.2476000040769577,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.13339999318122864,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.06859999895095825,"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/suite","display_name":"Suite","score":0.77559494972229},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.706099808216095},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.7048395276069641},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5294598937034607},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5071520805358887},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.48777300119400024},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4708896279335022},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36380207538604736},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.093097984790802}],"concepts":[{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.77559494972229},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.706099808216095},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.7048395276069641},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5294598937034607},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5071520805358887},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.48777300119400024},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4708896279335022},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36380207538604736},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.093097984790802},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"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":"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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","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":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti075","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti075","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/5/691/48962529/bioinformatics_21_5_691.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15531616","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15531616","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":"Bioinformatics (Oxford, England)","raw_type":"Evaluation Study"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti075","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti075","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/5/691/48962529/bioinformatics_21_5_691.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1999763852.pdf","grobid_xml":"https://content.openalex.org/works/W1999763852.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1558211564","https://openalex.org/W2074363252","https://openalex.org/W2123097295","https://openalex.org/W2142627516","https://openalex.org/W2158714788","https://openalex.org/W2166265186"],"related_works":["https://openalex.org/W4231704780","https://openalex.org/W2083794993","https://openalex.org/W352609212","https://openalex.org/W1511772879","https://openalex.org/W4200340037","https://openalex.org/W4379115841","https://openalex.org/W608917066","https://openalex.org/W4283652261","https://openalex.org/W585424826","https://openalex.org/W564602992"],"abstract_inverted_index":{"UNLABELLED:":[0],"ESTminer":[1],"is":[2,70],"a":[3,39,43,81,86],"collection":[4],"of":[5,33,42,88,93,102],"programs":[6,126],"that":[7,61],"use":[8],"expressed":[9],"sequence":[10,41],"tag":[11],"(EST)":[12],"data":[13],"from":[14,122],"inbred":[15,83],"genomes":[16],"to":[17,28,37,52,72,75,99,119],"identify":[18,76,100],"unique":[19,78],"genes":[20,121],"within":[21],"gene":[22,44],"families.":[23],"The":[24,125],"algorithm":[25,109],"utilizes":[26],"Cap3":[27],"perform":[29],"an":[30],"initial":[31],"clustering":[32],"related":[34,63],"EST":[35,59,74],"sequences":[36,48],"produce":[38],"consensus":[40,47],"family.":[45],"These":[46],"are":[49,62,132],"then":[50],"used":[51],"collect":[53],"all":[54],"ESTs":[55,89],"in":[56,129],"the":[57,91,103],"original":[58],"library":[60],"using":[64],"BLAST.":[65],"A":[66],"redundancy":[67],"based":[68],"criterion":[69],"applied":[71],"each":[73,97],"reliable":[77],"gene-sequences.":[79],"Using":[80],"highly":[82],"genome":[84],"as":[85],"source":[87],"eliminates":[90],"necessity":[92],"computing":[94],"covariance":[95],"on":[96],"polymorphism":[98],"alleles":[101],"same":[104],"gene,":[105],"thus":[106],"making":[107],"this":[108],"more":[110],"streamlined":[111],"than":[112],"other":[113],"alternatives":[114],"which":[115],"must":[116],"computationally":[117],"attempt":[118],"distinguish":[120],"alleles.":[123],"AVAILABILITY:":[124],"were":[127],"written":[128],"PERL":[130],"and":[131,142],"freely":[133],"available":[134],"at":[135],"http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html":[136],"CONTACT:":[137],"nelsonrt@iastate.edu":[138],"SUPPLEMENTARY":[139],"INFORMATION:":[140],"Figures":[141],"dataset":[143],"can":[144],"be":[145],"obtained":[146],"from:":[147],"http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html.":[148]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
