{"id":"https://openalex.org/W2113737058","doi":"https://doi.org/10.1109/ipdps.2003.1213286","title":"Using hybrid alignment for iterative sequence database searches","display_name":"Using hybrid alignment for iterative sequence database searches","publication_year":2004,"publication_date":"2004-03-22","ids":{"openalex":"https://openalex.org/W2113737058","doi":"https://doi.org/10.1109/ipdps.2003.1213286","mag":"2113737058"},"language":"en","primary_location":{"id":"doi:10.1109/ipdps.2003.1213286","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2003.1213286","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings International Parallel and Distributed Processing Symposium","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100652794","display_name":"Yuheng Li","orcid":"https://orcid.org/0000-0002-5971-8469"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuheng Li","raw_affiliation_strings":["Department of Computer and Information Science, Ohio State Uinversity, Columbus, OH, USA","Dept of Comput. & Inf. Sci., Ohio State Univ., Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science, Ohio State Uinversity, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Dept of Comput. & Inf. Sci., Ohio State Univ., Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026481712","display_name":"Mario Lauria","orcid":"https://orcid.org/0000-0001-5983-7292"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Lauria","raw_affiliation_strings":["Department of Computer and Information Science, Ohio State Uinversity, Columbus, OH, USA","Dept of Comput. & Inf. Sci., Ohio State Univ., Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science, Ohio State Uinversity, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Dept of Comput. & Inf. Sci., Ohio State Univ., Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044969846","display_name":"Ralf Bundschuh","orcid":"https://orcid.org/0000-0002-6699-8614"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. Bundschuh","raw_affiliation_strings":["Department of Physics, Ohio State Uinversity, Columbus, OH, USA","[Department of Physics, Ohio State Uinversity, Columbus, OH, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Ohio State Uinversity, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"[Department of Physics, Ohio State Uinversity, Columbus, OH, USA]","institution_ids":["https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I52357470"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"91","issue":null,"first_page":"8","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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":0.9986000061035156,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9890000224113464,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12073","display_name":"Isotope Analysis in Ecology","score":0.9832000136375427,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7091137766838074},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6687644720077515},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.6337155699729919},{"id":"https://openalex.org/keywords/iterative-refinement","display_name":"Iterative refinement","score":0.6174474954605103},{"id":"https://openalex.org/keywords/enhanced-data-rates-for-gsm-evolution","display_name":"Enhanced Data Rates for GSM Evolution","score":0.6150609850883484},{"id":"https://openalex.org/keywords/iterative-method","display_name":"Iterative method","score":0.5579913854598999},{"id":"https://openalex.org/keywords/position","display_name":"Position (finance)","score":0.48722949624061584},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.45100581645965576},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44735515117645264},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.41505905985832214},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3513919711112976},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29493990540504456},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10109215974807739}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7091137766838074},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6687644720077515},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.6337155699729919},{"id":"https://openalex.org/C2779982483","wikidata":"https://www.wikidata.org/wiki/Q6094420","display_name":"Iterative refinement","level":2,"score":0.6174474954605103},{"id":"https://openalex.org/C162307627","wikidata":"https://www.wikidata.org/wiki/Q204833","display_name":"Enhanced Data Rates for GSM Evolution","level":2,"score":0.6150609850883484},{"id":"https://openalex.org/C159694833","wikidata":"https://www.wikidata.org/wiki/Q2321565","display_name":"Iterative method","level":2,"score":0.5579913854598999},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.48722949624061584},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.45100581645965576},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44735515117645264},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.41505905985832214},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3513919711112976},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29493990540504456},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10109215974807739},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/ipdps.2003.1213286","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2003.1213286","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings International Parallel and Distributed Processing Symposium","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1483439120","https://openalex.org/W1659313070","https://openalex.org/W1983698816","https://openalex.org/W1988670311","https://openalex.org/W2006662402","https://openalex.org/W2015292449","https://openalex.org/W2015315215","https://openalex.org/W2026257220","https://openalex.org/W2026586467","https://openalex.org/W2032295681","https://openalex.org/W2034123395","https://openalex.org/W2045067706","https://openalex.org/W2054698853","https://openalex.org/W2055988139","https://openalex.org/W2057177664","https://openalex.org/W2070220641","https://openalex.org/W2072340282","https://openalex.org/W2076540369","https://openalex.org/W2085277871","https://openalex.org/W2089499735","https://openalex.org/W2094378111","https://openalex.org/W2094519647","https://openalex.org/W2102479256","https://openalex.org/W2115385703","https://openalex.org/W2117077088","https://openalex.org/W2120122292","https://openalex.org/W2126377763","https://openalex.org/W2133312664","https://openalex.org/W2139621307","https://openalex.org/W2140244239","https://openalex.org/W2143210482","https://openalex.org/W2145358391","https://openalex.org/W2155480346","https://openalex.org/W2157975034","https://openalex.org/W2158714788","https://openalex.org/W4235848672","https://openalex.org/W4246726420","https://openalex.org/W4252166161","https://openalex.org/W6682915077"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726","https://openalex.org/W2101418959"],"abstract_inverted_index":{"Progressive":[0],"sequence":[1,101],"model":[2],"refinement":[3],"by":[4],"means":[5],"of":[6,46,54,61,83,91,110,120],"iterative":[7,48],"searches":[8,17],"is":[9,19,74],"an":[10],"effective":[11],"technique":[12],"for":[13],"high":[14],"sensitivity":[15,45],"database":[16],"and":[18,28],"currently":[20],"employed":[21],"in":[22,58,99,114],"popular":[23],"tools":[24],"such":[25,47],"as":[26,79],"PSI-BLAST":[27],"SAM.":[29],"Recently,":[30],"a":[31,51,116],"novel":[32],"alignment":[33,72,81,102],"algorithm":[34,73],"has":[35],"been":[36],"proposed":[37,93],"that":[38,68,104],"offers":[39],"features":[40],"expected":[41],"to":[42,76,95,107],"improve":[43],"the":[44,59,69,80,89,111],"approaches,":[49],"specifically":[50],"well-characterized":[52],"theory":[53],"its":[55],"statistics":[56,103],"even":[57],"presence":[60],"position-specific":[62],"gap":[63],"costs.":[64],"Here,":[65],"we":[66,87],"demonstrate":[67],"new":[70],"hybrid":[71],"ready":[75],"be":[77,108],"used":[78],"core":[82],"PSI-BLAST.":[84,121],"In":[85],"addition,":[86],"evaluate":[88],"accuracy":[90],"two":[92],"approaches":[94],"edge":[96],"effect":[97],"correction":[98],"short":[100],"turns":[105],"out":[106],"one":[109],"crucial":[112],"issues":[113],"developing":[115],"hybrid-alignment":[117],"based":[118],"version":[119]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}