{"id":"https://openalex.org/W2121575926","doi":"https://doi.org/10.1177/1094342007078175","title":"Regular Paper: A Study of Architectural Optimization Methods in Bioinformatics Applications","display_name":"Regular Paper: A Study of Architectural Optimization Methods in Bioinformatics Applications","publication_year":2007,"publication_date":"2007-07-19","ids":{"openalex":"https://openalex.org/W2121575926","doi":"https://doi.org/10.1177/1094342007078175","mag":"2121575926"},"language":"en","primary_location":{"id":"doi:10.1177/1094342007078175","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342007078175","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"0890-2720","issn":["0890-2720","1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},"type":"article","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/A5056459929","display_name":"Guang\u2010Hong Tan","orcid":"https://orcid.org/0000-0002-6406-0331"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"G. Tan","raw_affiliation_strings":["KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF\r                        COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA,","Key Laboratory of Computer System and Architecture, Institute of Computing Technology, Chinese Academy of Sciences Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF\r                        COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA,","institution_ids":["https://openalex.org/I4210090176"]},{"raw_affiliation_string":"Key Laboratory of Computer System and Architecture, Institute of Computing Technology, Chinese Academy of Sciences Beijing, China","institution_ids":["https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045330783","display_name":"Lin Xu","orcid":"https://orcid.org/0000-0003-2602-9875"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"L. Xu","raw_affiliation_strings":["KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF\r                        COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA","Key Laboratory of Computer System and Architecture, Institute of Computing Technology, Chinese Academy of Sciences Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF\r                        COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA","institution_ids":["https://openalex.org/I4210090176"]},{"raw_affiliation_string":"Key Laboratory of Computer System and Architecture, Institute of Computing Technology, Chinese Academy of Sciences Beijing, China","institution_ids":["https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089850097","display_name":"Zhong\u2010Min Dai","orcid":"https://orcid.org/0000-0003-4083-1901"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Z. Dai","raw_affiliation_strings":["KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF\r                        COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA","Key Laboratory of Computer System and Architecture, Institute of Computing Technology, Chinese Academy of Sciences Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF\r                        COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA","institution_ids":["https://openalex.org/I4210090176"]},{"raw_affiliation_string":"Key Laboratory of Computer System and Architecture, Institute of Computing Technology, Chinese Academy of Sciences Beijing, China","institution_ids":["https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101952645","display_name":"Shengzhong Feng","orcid":"https://orcid.org/0000-0002-6225-2815"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"S. Feng","raw_affiliation_strings":["KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF\r                        COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA","Key Laboratory of Computer System and Architecture, Institute of Computing Technology, Chinese Academy of Sciences Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF\r                        COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA","institution_ids":["https://openalex.org/I4210090176"]},{"raw_affiliation_string":"Key Laboratory of Computer System and Architecture, Institute of Computing Technology, Chinese Academy of Sciences Beijing, China","institution_ids":["https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101738013","display_name":"Ninghui Sun","orcid":"https://orcid.org/0000-0002-1953-1392"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"N. Sun","raw_affiliation_strings":["KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF\r                        COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA","Key Laboratory of Computer System and Architecture, Institute of Computing Technology, Chinese Academy of Sciences Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF\r                        COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA","institution_ids":["https://openalex.org/I4210090176"]},{"raw_affiliation_string":"Key Laboratory of Computer System and Architecture, Institute of Computing Technology, Chinese Academy of Sciences Beijing, China","institution_ids":["https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5056459929"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176"],"apc_list":null,"apc_paid":null,"fwci":0.2515,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.57266884,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"3","first_page":"371","last_page":"384"},"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/T11269","display_name":"Algorithms and Data Compression","score":0.9962000250816345,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9884999990463257,"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/computer-science","display_name":"Computer science","score":0.7852881550788879},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6439883708953857},{"id":"https://openalex.org/keywords/cache","display_name":"Cache","score":0.6083164215087891},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.584800124168396},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.41940224170684814},{"id":"https://openalex.org/keywords/optimization-algorithm","display_name":"Optimization algorithm","score":0.41637134552001953},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.20544558763504028},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.10516232252120972},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.06937500834465027}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7852881550788879},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6439883708953857},{"id":"https://openalex.org/C115537543","wikidata":"https://www.wikidata.org/wiki/Q165596","display_name":"Cache","level":2,"score":0.6083164215087891},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.584800124168396},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.41940224170684814},{"id":"https://openalex.org/C2987595161","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Optimization algorithm","level":2,"score":0.41637134552001953},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.20544558763504028},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.10516232252120972},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.06937500834465027}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1177/1094342007078175","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342007078175","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"0890-2720","issn":["0890-2720","1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320308928","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1538592187","https://openalex.org/W1555915743","https://openalex.org/W1866830630","https://openalex.org/W1990061958","https://openalex.org/W2055043387","https://openalex.org/W2055666215","https://openalex.org/W2087064593","https://openalex.org/W2096108516","https://openalex.org/W2102182691","https://openalex.org/W2106882534","https://openalex.org/W2130289795","https://openalex.org/W2132967231","https://openalex.org/W2133098231","https://openalex.org/W2133782309","https://openalex.org/W2136952590","https://openalex.org/W2141697594","https://openalex.org/W2148542244","https://openalex.org/W2155350341","https://openalex.org/W2157909358","https://openalex.org/W2320748401","https://openalex.org/W2725179571","https://openalex.org/W2788962374","https://openalex.org/W4233075742","https://openalex.org/W4236957397","https://openalex.org/W4255763627"],"related_works":["https://openalex.org/W2152099439","https://openalex.org/W4231775656","https://openalex.org/W1984163603","https://openalex.org/W3130422087","https://openalex.org/W2383646825","https://openalex.org/W2371018915","https://openalex.org/W3004195166","https://openalex.org/W1563139915","https://openalex.org/W2885669284","https://openalex.org/W4301184821"],"abstract_inverted_index":{"Studies":[0],"in":[1,11],"the":[2,66],"optimization":[3,67],"of":[4],"sequence":[5],"alignment":[6],"have":[7,17,35,54,62,76],"been":[8,55,63,69,77],"carried":[9],"out":[10],"bioinformatics.":[12],"In":[13],"this":[14],"paper,":[15],"we":[16],"focused":[18],"on":[19,39,73],"two":[20],"aspects:":[21],"memory":[22,32],"usage":[23],"and":[24,57],"execution":[25],"time.":[26],"Our":[27,42],"study":[28],"suggests":[29],"that":[30],"cache":[31],"does":[33],"not":[34],"a":[36],"significant":[37],"effect":[38],"system":[40,74,83],"performance.":[41],"attention":[43],"then":[44],"turns":[45],"to":[46],"optimize":[47],"Smith\u2014Waterman's":[48],"algorithm.":[49],"Two":[50],"instruction":[51],"level":[52],"methods":[53],"proposed":[56],"2\u20148":[58],"fold":[59],"speed":[60],"improvements":[61,72],"observed":[64],"after":[65],"has":[68],"implemented.":[70],"Further":[71],"performance":[75],"achieved":[78],"by":[79],"overlapping":[80],"computation":[81],"with":[82],"I/O":[84],"usage.":[85]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}
