{"id":"https://openalex.org/W4295500606","doi":"https://doi.org/10.1109/embc48229.2022.9870924","title":"Hardware-Algorithm Codesign for Fast and Energy Efficient Approximate String Matching on FPGA for Computational Biology","display_name":"Hardware-Algorithm Codesign for Fast and Energy Efficient Approximate String Matching on FPGA for Computational Biology","publication_year":2022,"publication_date":"2022-07-11","ids":{"openalex":"https://openalex.org/W4295500606","doi":"https://doi.org/10.1109/embc48229.2022.9870924","pmid":"https://pubmed.ncbi.nlm.nih.gov/36086088"},"language":"en","primary_location":{"id":"doi:10.1109/embc48229.2022.9870924","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc48229.2022.9870924","pdf_url":null,"source":{"id":"https://openalex.org/S4363607706","display_name":"2022 44th Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 44th Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5079401295","display_name":"Venkateshwarlu Y. Gudur","orcid":"https://orcid.org/0000-0002-6476-7222"},"institutions":[{"id":"https://openalex.org/I65181880","display_name":"Indian Institute of Technology Hyderabad","ror":"https://ror.org/01j4v3x97","country_code":"IN","type":"education","lineage":["https://openalex.org/I65181880"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Venkateshwarlu Yellaswamy Gudur","raw_affiliation_strings":["Indian Institute of Technology Hyderabad,Department of Electrical Engineering,Telangana,India,502285"],"affiliations":[{"raw_affiliation_string":"Indian Institute of Technology Hyderabad,Department of Electrical Engineering,Telangana,India,502285","institution_ids":["https://openalex.org/I65181880"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061841041","display_name":"Sidharth Maheshwari","orcid":"https://orcid.org/0000-0002-9665-5698"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sidharth Maheshwari","raw_affiliation_strings":["School of Engineering, Newcastle University,UK,NE1 7RU"],"affiliations":[{"raw_affiliation_string":"School of Engineering, Newcastle University,UK,NE1 7RU","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087944991","display_name":"Swati Bhardwaj","orcid":"https://orcid.org/0000-0001-9534-8808"},"institutions":[{"id":"https://openalex.org/I65181880","display_name":"Indian Institute of Technology Hyderabad","ror":"https://ror.org/01j4v3x97","country_code":"IN","type":"education","lineage":["https://openalex.org/I65181880"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Swati Bhardwaj","raw_affiliation_strings":["Indian Institute of Technology Hyderabad,Department of Electrical Engineering,Telangana,India,502285"],"affiliations":[{"raw_affiliation_string":"Indian Institute of Technology Hyderabad,Department of Electrical Engineering,Telangana,India,502285","institution_ids":["https://openalex.org/I65181880"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044085104","display_name":"Amit Acharyya","orcid":"https://orcid.org/0000-0002-5636-0676"},"institutions":[{"id":"https://openalex.org/I65181880","display_name":"Indian Institute of Technology Hyderabad","ror":"https://ror.org/01j4v3x97","country_code":"IN","type":"education","lineage":["https://openalex.org/I65181880"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Amit Acharyya","raw_affiliation_strings":["Indian Institute of Technology Hyderabad,Department of Electrical Engineering,Telangana,India,502285"],"affiliations":[{"raw_affiliation_string":"Indian Institute of Technology Hyderabad,Department of Electrical Engineering,Telangana,India,502285","institution_ids":["https://openalex.org/I65181880"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077777787","display_name":"Rishad Shafik","orcid":"https://orcid.org/0000-0001-5444-537X"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rishad Shafik","raw_affiliation_strings":["School of Engineering, Newcastle University,UK,NE1 7RU"],"affiliations":[{"raw_affiliation_string":"School of Engineering, Newcastle University,UK,NE1 7RU","institution_ids":["https://openalex.org/I84884186"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5079401295"],"corresponding_institution_ids":["https://openalex.org/I65181880"],"apc_list":null,"apc_paid":null,"fwci":0.2078,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.4116031,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"2022","issue":null,"first_page":"87","last_page":"90"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9991999864578247,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9991999864578247,"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/T12326","display_name":"Network Packet Processing and Optimization","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.994700014591217,"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":0.7495003342628479},{"id":"https://openalex.org/keywords/approximate-string-matching","display_name":"Approximate string matching","score":0.6500840187072754},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.636970579624176},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5890165567398071},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"Hardware acceleration","score":0.572218120098114},{"id":"https://openalex.org/keywords/string-searching-algorithm","display_name":"String searching algorithm","score":0.5653347969055176},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5355712175369263},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.48338642716407776},{"id":"https://openalex.org/keywords/efficient-energy-use","display_name":"Efficient energy use","score":0.4546308219432831},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.4386008679866791},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.42363405227661133},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.3432254195213318},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.2636431157588959},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14429971575737},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13231348991394043},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1150970458984375}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7495003342628479},{"id":"https://openalex.org/C32610155","wikidata":"https://www.wikidata.org/wiki/Q1798621","display_name":"Approximate string matching","level":3,"score":0.6500840187072754},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.636970579624176},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5890165567398071},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.572218120098114},{"id":"https://openalex.org/C7757238","wikidata":"https://www.wikidata.org/wiki/Q374040","display_name":"String searching algorithm","level":3,"score":0.5653347969055176},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5355712175369263},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.48338642716407776},{"id":"https://openalex.org/C2742236","wikidata":"https://www.wikidata.org/wiki/Q924713","display_name":"Efficient energy use","level":2,"score":0.4546308219432831},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.4386008679866791},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.42363405227661133},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.3432254195213318},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.2636431157588959},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14429971575737},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13231348991394043},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1150970458984375},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","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":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003246","descriptor_name":"Conservation of Energy Resources","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003246","descriptor_name":"Conservation of Energy Resources","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003246","descriptor_name":"Conservation of Energy Resources","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/embc48229.2022.9870924","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc48229.2022.9870924","pdf_url":null,"source":{"id":"https://openalex.org/S4363607706","display_name":"2022 44th Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 44th Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","raw_type":"proceedings-article"},{"id":"pmid:36086088","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36086088","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8999999761581421,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320295","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W2011218124","https://openalex.org/W2028431438","https://openalex.org/W2034798008","https://openalex.org/W2052601433","https://openalex.org/W2099028196","https://openalex.org/W2100751585","https://openalex.org/W2104846587","https://openalex.org/W2153923325","https://openalex.org/W2264337508","https://openalex.org/W2585711475","https://openalex.org/W2606268188","https://openalex.org/W2620825407","https://openalex.org/W2730366953","https://openalex.org/W2745824628","https://openalex.org/W2766569692","https://openalex.org/W2799204259","https://openalex.org/W2988054748","https://openalex.org/W3006629507","https://openalex.org/W3193826708","https://openalex.org/W6693180885","https://openalex.org/W6740311864"],"related_works":["https://openalex.org/W2371263218","https://openalex.org/W2257399947","https://openalex.org/W3145288231","https://openalex.org/W2386746909","https://openalex.org/W2502807948","https://openalex.org/W2037600093","https://openalex.org/W2141423589","https://openalex.org/W2378689532","https://openalex.org/W2178786736","https://openalex.org/W2399644331"],"abstract_inverted_index":{"Myers":[0,86],"bit-vector":[1,87],"algorithm":[2,88,119],"for":[3,60,89,111],"approximate":[4],"string":[5],"matching":[6],"(ASM)":[7],"is":[8,21,39],"a":[9,80,135],"dynamic":[10],"programming":[11],"based":[12,84],"approach":[13],"that":[14],"takes":[15],"advantage":[16],"of":[17,23,44,56,67,72,92,117,139],"bit-parallel":[18],"operations.":[19],"It":[20],"one":[22],"the":[24,29,45,57,64,70,97,127],"fastest":[25],"algorithms":[26,59],"to":[27],"find":[28],"edit":[30],"distance":[31],"between":[32],"two":[33],"strings.":[34],"In":[35,75,122],"computational":[36,46],"biology,":[37],"ASM":[38,61,82,118],"used":[40],"at":[41],"various":[42],"stages":[43],"pipeline,":[47],"including":[48],"proteomics":[49],"and":[50,108,114],"genomics.":[51],"The":[52,100],"computationally":[53],"intensive":[54],"nature":[55],"underlying":[58],"operating":[62],"on":[63,85,120],"large":[65],"volume":[66],"data":[68],"necessitates":[69],"acceleration":[71],"these":[73],"algorithms.":[74],"this":[76],"paper,":[77],"we":[78],"propose":[79],"novel":[81],"architecture":[83,103],"parallel":[90,102],"searching":[91],"multiple":[93,105],"query":[94],"patterns":[95],"in":[96],"biological":[98],"databases.":[99],"proposed":[101,128],"uses":[104],"processing":[106],"engines":[107],"hardware/software":[109],"codesign":[110],"an":[112],"accelerated":[113],"energy-efficient":[115],"design":[116,129],"hardware.":[121],"comparison":[123],"with":[124,134],"related":[125],"literature,":[126],"achieves":[130],"22\u00d7":[131],"better":[132],"performance":[133],"demonstrative":[136],"energy":[137],"efficiency":[138],"\u223c":[140],"500\u00d710<sup>9</sup>":[141],"cell":[142],"updates":[143],"per":[144],"joule.":[145]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
