{"id":"https://openalex.org/W2043866155","doi":"https://doi.org/10.1109/tcbb.2014.2366112","title":"Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate","display_name":"Improving Retrieval Efficacy of Homology Searches Using the False Discovery Rate","publication_year":2014,"publication_date":"2014-10-30","ids":{"openalex":"https://openalex.org/W2043866155","doi":"https://doi.org/10.1109/tcbb.2014.2366112","mag":"2043866155","pmid":"https://pubmed.ncbi.nlm.nih.gov/26357264"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2366112","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2366112","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4568567","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065514255","display_name":"Hyrum Carroll","orcid":"https://orcid.org/0000-0002-1917-2131"},"institutions":[{"id":"https://openalex.org/I169615421","display_name":"Middle Tennessee State University","ror":"https://ror.org/02n1hzn07","country_code":"US","type":"education","lineage":["https://openalex.org/I169615421"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hyrum D. Carroll","raw_affiliation_strings":["Department of Computer Science, Middle Tennessee State University, Murfreesboro, TN","Dept. of Computer Science, Middle Tennessee State University, Murfreesboro, TN#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Middle Tennessee State University, Murfreesboro, TN","institution_ids":["https://openalex.org/I169615421"]},{"raw_affiliation_string":"Dept. of Computer Science, Middle Tennessee State University, Murfreesboro, TN#TAB#","institution_ids":["https://openalex.org/I169615421"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005700214","display_name":"Alex C. Williams","orcid":"https://orcid.org/0000-0002-1412-6347"},"institutions":[{"id":"https://openalex.org/I169615421","display_name":"Middle Tennessee State University","ror":"https://ror.org/02n1hzn07","country_code":"US","type":"education","lineage":["https://openalex.org/I169615421"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alex C. Williams","raw_affiliation_strings":["Department of Computer Science, Middle Tennessee State University, Murfreesboro, TN","Dept. of Computer Science, Middle Tennessee State University, Murfreesboro, TN#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Middle Tennessee State University, Murfreesboro, TN","institution_ids":["https://openalex.org/I169615421"]},{"raw_affiliation_string":"Dept. of Computer Science, Middle Tennessee State University, Murfreesboro, TN#TAB#","institution_ids":["https://openalex.org/I169615421"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058812543","display_name":"Anthony G. Davis","orcid":null},"institutions":[{"id":"https://openalex.org/I169615421","display_name":"Middle Tennessee State University","ror":"https://ror.org/02n1hzn07","country_code":"US","type":"education","lineage":["https://openalex.org/I169615421"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anthony G. Davis","raw_affiliation_strings":["Department of Computer Science, Middle Tennessee State University, Murfreesboro, TN","Dept. of Computer Science, Middle Tennessee State University, Murfreesboro, TN#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Middle Tennessee State University, Murfreesboro, TN","institution_ids":["https://openalex.org/I169615421"]},{"raw_affiliation_string":"Dept. of Computer Science, Middle Tennessee State University, Murfreesboro, TN#TAB#","institution_ids":["https://openalex.org/I169615421"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039386346","display_name":"John L. Spouge","orcid":"https://orcid.org/0000-0001-6207-1419"},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John L. Spouge","raw_affiliation_strings":["National Center for Biotechnology Information, Bethesda, MD"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, Bethesda, MD","institution_ids":["https://openalex.org/I4210109390"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":0.1299,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.50529698,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"12","issue":"3","first_page":"531","last_page":"537"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.996999979019165,"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":0.996999979019165,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9966999888420105,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9782000184059143,"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/false-discovery-rate","display_name":"False discovery rate","score":0.745388388633728},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.593120276927948},{"id":"https://openalex.org/keywords/statistic","display_name":"Statistic","score":0.5736077427864075},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4203764796257019},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35679349303245544},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3314535617828369},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2774205803871155},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2368677258491516},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11149922013282776}],"concepts":[{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.745388388633728},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.593120276927948},{"id":"https://openalex.org/C89128539","wikidata":"https://www.wikidata.org/wiki/Q1949963","display_name":"Statistic","level":2,"score":0.5736077427864075},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4203764796257019},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35679349303245544},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3314535617828369},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2774205803871155},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2368677258491516},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11149922013282776},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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},{"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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbb.2014.2366112","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2366112","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26357264","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26357264","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4568567","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4568567","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"IEEE/ACM Trans Comput Biol Bioinform","raw_type":"Text"},{"id":"pmh:oai:csuepress.columbusstate.edu:bibliography_faculty-4326","is_oa":false,"landing_page_url":"https://csuepress.columbusstate.edu/bibliography_faculty/3380","pdf_url":null,"source":{"id":"https://openalex.org/S4377196711","display_name":"CSU ePress (Columbus State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I199172307","host_organization_name":"Columbus State University","host_organization_lineage":["https://openalex.org/I199172307"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Bibliography","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4568567","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4568567","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"IEEE/ACM Trans Comput Biol Bioinform","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1240387827","display_name":"Statistical Evaluation of Retrieval Efficiency from Data","funder_award_id":"1z01lm000094-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3917585121","display_name":"BIBLIOMETRIC APPLICATIONS IN BIOMEDICAL INFORMATION","funder_award_id":"7k04lm000088-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1966570126","https://openalex.org/W1969465720","https://openalex.org/W2036714085","https://openalex.org/W2043887901","https://openalex.org/W2062296203","https://openalex.org/W2084787613","https://openalex.org/W2105381419","https://openalex.org/W2107757325","https://openalex.org/W2110065044","https://openalex.org/W2115012618","https://openalex.org/W2121044470","https://openalex.org/W2133657429","https://openalex.org/W2139271731","https://openalex.org/W2140821974","https://openalex.org/W2158714788","https://openalex.org/W2172016350","https://openalex.org/W2606759007","https://openalex.org/W4253158681"],"related_works":["https://openalex.org/W2389124870","https://openalex.org/W1921844237","https://openalex.org/W2168149717","https://openalex.org/W200978175","https://openalex.org/W2178204436","https://openalex.org/W2113356685","https://openalex.org/W4300887971","https://openalex.org/W4293336298","https://openalex.org/W2467227750","https://openalex.org/W2118778496"],"abstract_inverted_index":{"Over":[0],"the":[1,36,49,69,79,100,141,147,153],"past":[2],"few":[3],"decades,":[4],"discovery":[5,71],"based":[6],"on":[7,131,166],"sequence":[8],"homology":[9,113],"has":[10,24,40],"become":[11],"a":[12,76,104,132,167],"widely":[13],"accepted":[14],"practice.":[15],"Consequently,":[16],"comparative":[17],"accuracy":[18],"of":[19,33,48,102,122],"retrieval":[20,34,89,123,162,179],"algorithms":[21],"(e.g.,":[22],"BLAST)":[23],"been":[25],"rigorously":[26],"studied":[27],"for":[28,78],"improvement.":[29],"Unlike":[30],"most":[31],"components":[32],"algorithms,":[35],"E-value":[37],"threshold":[38,50,81,154],"criterion":[39,82],"yet":[41],"to":[42,85,188],"be":[43],"thoroughly":[44],"investigated.":[45],"An":[46],"investigation":[47],"is":[51],"important":[52],"as":[53,75,146],"it":[54],"exclusively":[55],"dictates":[56],"which":[57],"sequences":[58],"are":[59,194],"declared":[60],"relevant":[61],"and":[62,94,110,173,190,192],"irrelevant.":[63],"In":[64],"this":[65],"paper,":[66],"we":[67,98,118,139],"introduce":[68],"false":[70],"rate":[72],"(FDR)":[73],"statistic":[74],"replacement":[77,105],"uniform":[80],"in":[83,88,106],"order":[84],"improve":[86],"efficacy":[87,124],"systems.":[90],"Using":[91],"NCBI's":[92],"BLAST":[93,165],"PSI-BLAST":[95],"software":[96],"packages,":[97],"demonstrate":[99],"applicability":[101],"such":[103],"both":[107],"non-iterative":[108],"(BLASTFDR)":[109],"iterative":[111],"(PSI-BLAST(FDR))":[112],"searches.":[114],"For":[115,136],"each":[116,137],"application,":[117],"performed":[119],"an":[120],"evaluation":[121],"with":[125],"five":[126],"different":[127],"multiple":[128],"testing":[129],"methods":[130],"large":[133,168],"training":[134],"database.":[135],"algorithm,":[138],"choose":[140],"best":[142],"performing":[143],"method,":[144],"Benjamini-Hochberg,":[145],"default":[148],"statistic.":[149],"As":[150],"measured":[151],"by":[152],"average":[155],"precision,":[156],"BLAST(FDR)":[157,189],"yielded":[158],"14.1":[159],"percent":[160,177],"better":[161,178],"performance":[163,180],"than":[164,181],"(5,161":[169],"queries)":[170],"test":[171],"database":[172],"PSI-BLAST(FDR)":[174,191],"attained":[175],"11.8":[176],"PSI-BLAST.":[182],"The":[183],"C++":[184],"source":[185],"code":[186],"specific":[187],"instructions":[193],"available":[195],"at":[196],"http://www.cs.mtsu.edu/~hcarroll/blast_fdr/.":[197]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
