{"id":"https://openalex.org/W2139050912","doi":"https://doi.org/10.1109/bibe.2004.1317395","title":"Indexing genomic databases","display_name":"Indexing genomic databases","publication_year":2004,"publication_date":"2004-11-30","ids":{"openalex":"https://openalex.org/W2139050912","doi":"https://doi.org/10.1109/bibe.2004.1317395","mag":"2139050912"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2004.1317395","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2004.1317395","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://works.bepress.com/dan_krane/20","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110451200","display_name":"Gina Cooper","orcid":null},"institutions":[{"id":"https://openalex.org/I19648265","display_name":"Wright State University","ror":"https://ror.org/04qk6pt94","country_code":"US","type":"education","lineage":["https://openalex.org/I19648265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G. Cooper","raw_affiliation_strings":["Wright State University, Dayton, OH, USA","Wright State Univ., Dayton, OH, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wright State University, Dayton, OH, USA","institution_ids":["https://openalex.org/I19648265"]},{"raw_affiliation_string":"Wright State Univ., Dayton, OH, USA#TAB#","institution_ids":["https://openalex.org/I19648265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021570308","display_name":"Michael L. Raymer","orcid":null},"institutions":[{"id":"https://openalex.org/I19648265","display_name":"Wright State University","ror":"https://ror.org/04qk6pt94","country_code":"US","type":"education","lineage":["https://openalex.org/I19648265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Raymer","raw_affiliation_strings":["Wright State University, Dayton, OH, USA","Wright State Univ., Dayton, OH, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wright State University, Dayton, OH, USA","institution_ids":["https://openalex.org/I19648265"]},{"raw_affiliation_string":"Wright State Univ., Dayton, OH, USA#TAB#","institution_ids":["https://openalex.org/I19648265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032815885","display_name":"Travis E. Doom","orcid":null},"institutions":[{"id":"https://openalex.org/I19648265","display_name":"Wright State University","ror":"https://ror.org/04qk6pt94","country_code":"US","type":"education","lineage":["https://openalex.org/I19648265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. Doom","raw_affiliation_strings":["Wright State University, Dayton, OH, USA","Wright State Univ., Dayton, OH, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wright State University, Dayton, OH, USA","institution_ids":["https://openalex.org/I19648265"]},{"raw_affiliation_string":"Wright State Univ., Dayton, OH, USA#TAB#","institution_ids":["https://openalex.org/I19648265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088426272","display_name":"Dan E. Krane","orcid":null},"institutions":[{"id":"https://openalex.org/I19648265","display_name":"Wright State University","ror":"https://ror.org/04qk6pt94","country_code":"US","type":"education","lineage":["https://openalex.org/I19648265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Krane","raw_affiliation_strings":["Wright State University, Dayton, OH, USA","Wright State Univ., Dayton, OH, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wright State University, Dayton, OH, USA","institution_ids":["https://openalex.org/I19648265"]},{"raw_affiliation_string":"Wright State Univ., Dayton, OH, USA#TAB#","institution_ids":["https://openalex.org/I19648265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015233889","display_name":"Natsuhiko Futamura","orcid":null},"institutions":[{"id":"https://openalex.org/I19648265","display_name":"Wright State University","ror":"https://ror.org/04qk6pt94","country_code":"US","type":"education","lineage":["https://openalex.org/I19648265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"N. Futamura","raw_affiliation_strings":["Wright State University, Dayton, OH, USA","Wright State Univ., Dayton, OH, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wright State University, Dayton, OH, USA","institution_ids":["https://openalex.org/I19648265"]},{"raw_affiliation_string":"Wright State Univ., Dayton, OH, USA#TAB#","institution_ids":["https://openalex.org/I19648265"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2412,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.55429907,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"587","last_page":"591"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983000159263611,"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":0.9983000159263611,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9866999983787537,"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/search-engine-indexing","display_name":"Search engine indexing","score":0.8881232738494873},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7989963293075562},{"id":"https://openalex.org/keywords/relational-database-management-system","display_name":"Relational database management system","score":0.6189994812011719},{"id":"https://openalex.org/keywords/database-index","display_name":"Database index","score":0.5800986289978027},{"id":"https://openalex.org/keywords/scheme","display_name":"Scheme (mathematics)","score":0.576524019241333},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5594383478164673},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5451175570487976},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5223758816719055},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.4529317021369934},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.440179705619812},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4006776809692383},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.09019869565963745},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08981546759605408},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07042089104652405}],"concepts":[{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.8881232738494873},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7989963293075562},{"id":"https://openalex.org/C24394798","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database management system","level":3,"score":0.6189994812011719},{"id":"https://openalex.org/C59276292","wikidata":"https://www.wikidata.org/wiki/Q580427","display_name":"Database index","level":3,"score":0.5800986289978027},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.576524019241333},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5594383478164673},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5451175570487976},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5223758816719055},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.4529317021369934},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.440179705619812},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4006776809692383},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.09019869565963745},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08981546759605408},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07042089104652405},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1109/bibe.2004.1317395","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2004.1317395","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering","raw_type":"proceedings-article"},{"id":"pmh:oai:corescholar.libraries.wright.edu:knoesis-2297","is_oa":false,"landing_page_url":"https://corescholar.libraries.wright.edu/knoesis/921","pdf_url":null,"source":{"id":"https://openalex.org/S2737205702","display_name":"Journal of Bioresource Management","issn_l":"2309-3854","issn":["2309-3854"],"is_oa":false,"is_in_doaj":true,"is_core":false,"host_organization":"https://openalex.org/P4310316536","host_organization_name":"Bioresource Research Center (BRC), Islamabad","host_organization_lineage":["https://openalex.org/P4310316536"],"host_organization_lineage_names":["Bioresource Research Center (BRC), Islamabad"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Kno.e.sis Publications","raw_type":"text"},{"id":"pmh:oai:works.bepress.com:dan_krane-1019","is_oa":true,"landing_page_url":"https://works.bepress.com/dan_krane/20","pdf_url":null,"source":{"id":"https://openalex.org/S2737205702","display_name":"Journal of Bioresource Management","issn_l":"2309-3854","issn":["2309-3854"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":"https://openalex.org/P4310316536","host_organization_name":"Bioresource Research Center (BRC), Islamabad","host_organization_lineage":["https://openalex.org/P4310316536"],"host_organization_lineage_names":["Bioresource Research Center (BRC), Islamabad"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Dan E. Krane","raw_type":"text"},{"id":"pmh:oai:works.bepress.com:michael_raymer-1019","is_oa":false,"landing_page_url":"https://works.bepress.com/michael_raymer/20","pdf_url":null,"source":{"id":"https://openalex.org/S4306400146","display_name":"CORE Scholar (Wright State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I19648265","host_organization_name":"Wright State University","host_organization_lineage":["https://openalex.org/I19648265"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Michael L. Raymer","raw_type":"text"},{"id":"pmh:oai:works.bepress.com:travis_doom-1012","is_oa":true,"landing_page_url":"https://works.bepress.com/travis_doom/13","pdf_url":null,"source":{"id":"https://openalex.org/S2737205702","display_name":"Journal of Bioresource Management","issn_l":"2309-3854","issn":["2309-3854"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":"https://openalex.org/P4310316536","host_organization_name":"Bioresource Research Center (BRC), Islamabad","host_organization_lineage":["https://openalex.org/P4310316536"],"host_organization_lineage_names":["Bioresource Research Center (BRC), Islamabad"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Travis E. Doom","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:works.bepress.com:dan_krane-1019","is_oa":true,"landing_page_url":"https://works.bepress.com/dan_krane/20","pdf_url":null,"source":{"id":"https://openalex.org/S2737205702","display_name":"Journal of Bioresource Management","issn_l":"2309-3854","issn":["2309-3854"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":"https://openalex.org/P4310316536","host_organization_name":"Bioresource Research Center (BRC), Islamabad","host_organization_lineage":["https://openalex.org/P4310316536"],"host_organization_lineage_names":["Bioresource Research Center (BRC), Islamabad"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Dan E. Krane","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W1972784262","https://openalex.org/W2015292449","https://openalex.org/W2030428223","https://openalex.org/W2055043387","https://openalex.org/W2075026875","https://openalex.org/W2087064593","https://openalex.org/W2993766332","https://openalex.org/W4236236547"],"related_works":["https://openalex.org/W2505630977","https://openalex.org/W2383709723","https://openalex.org/W1567213510","https://openalex.org/W2626533837","https://openalex.org/W1505866794","https://openalex.org/W2527247821","https://openalex.org/W2375584934","https://openalex.org/W2761120596","https://openalex.org/W1575529579","https://openalex.org/W2525788546"],"abstract_inverted_index":{"Current":[0],"biological":[1],"sequence":[2,23],"comparison":[3],"tools":[4],"utilize":[5],"full":[6],"database":[7,15,31],"searches":[8],"to":[9,22,69,87],"find":[10],"approximate":[11],"matches":[12],"between":[13],"a":[14,17,33,66],"and":[16,49,82,105,120],"query.":[18],"A":[19],"new":[20],"approach":[21],"comparisons":[24],"can":[25,40],"be":[26],"performed":[27],"by":[28],"indexing":[29,35,115],"the":[30,89,94,98],"using":[32],"novel":[34],"scheme.":[36],"An":[37],"indexed":[38,56],"scheme":[39],"immediately":[41],"eliminate":[42],"highly":[43],"mismatched":[44],"sequences":[45],"thereby":[46],"improving":[47],"performance":[48],"accuracy.":[50],"iBlast":[51,64],"is":[52],"proposed":[53],"as":[54],"an":[55,74],"version":[57],"of":[58,80,97],"BLAST.":[59],"In":[60],"its":[61],"initial":[62],"implementation,":[63],"uses":[65],"sequence-based":[67],"index":[68],"catalog":[70],"genomic":[71],"databases":[72],"in":[73,108,111],"NCR":[75],"Teradata":[76,99],"RDBMS.":[77],"Several":[78],"types":[79],"indexes":[81],"querying":[83],"methods":[84,116],"are":[85,106,124],"explored":[86],"determine":[88],"most":[90],"efficient":[91],"solution":[92],"utilizing":[93],"parallel":[95],"nature":[96],"system.":[100],"Significant":[101],"speedups":[102],"were":[103],"obtained":[104],"explained":[107],"further":[109],"detail":[110],"this":[112],"paper.":[113],"Future":[114],"based":[117],"on":[118],"prokaryotic":[119],"eukaryotic":[121],"genome":[122],"structures":[123],"also":[125],"proposed.":[126]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
