{"id":"https://openalex.org/W2115069592","doi":"https://doi.org/10.1109/fpl.2007.4380764","title":"A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP","display_name":"A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP","publication_year":2007,"publication_date":"2007-08-01","ids":{"openalex":"https://openalex.org/W2115069592","doi":"https://doi.org/10.1109/fpl.2007.4380764","mag":"2115069592"},"language":"en","primary_location":{"id":"doi:10.1109/fpl.2007.4380764","is_oa":false,"landing_page_url":"https://doi.org/10.1109/fpl.2007.4380764","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 International Conference on Field Programmable Logic and Applications","raw_type":"proceedings-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/A5022151805","display_name":"Brandon Harris","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brandon Harris","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University, Saint Louis, USA","Washington University in St. Louis (St. Louis)"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University, Saint Louis, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Washington University in St. Louis (St. Louis)","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105839606","display_name":"Arpith C. Jacob","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arpith C. Jacob","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University, Saint Louis, USA","Washington University in St. Louis (St. Louis)"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University, Saint Louis, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Washington University in St. Louis (St. Louis)","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050179788","display_name":"Joseph M. Lancaster","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph M. Lancaster","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University, Saint Louis, USA","Washington University in St. Louis (St. Louis)"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University, Saint Louis, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Washington University in St. Louis (St. Louis)","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080937008","display_name":"Jeremy Buhler","orcid":"https://orcid.org/0000-0002-4159-4226"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy Buhler","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University, Saint Louis, USA","Washington University in St. Louis (St. Louis)"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University, Saint Louis, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Washington University in St. Louis (St. Louis)","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006814645","display_name":"Roger D. Chamberlain","orcid":"https://orcid.org/0000-0002-7207-6106"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roger D. Chamberlain","raw_affiliation_strings":["Department of Computer Science and Engineering, Washington University, Saint Louis, USA","Washington University in St. Louis (St. Louis)"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Washington University, Saint Louis, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Washington University in St. Louis (St. Louis)","institution_ids":["https://openalex.org/I204465549"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5022151805"],"corresponding_institution_ids":["https://openalex.org/I204465549"],"apc_list":null,"apc_paid":null,"fwci":3.8855,"has_fulltext":false,"cited_by_count":49,"citation_normalized_percentile":{"value":0.93675104,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"765","last_page":"769"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9993000030517578,"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":0.9993000030517578,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983999729156494,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.8326138257980347},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.7168453931808472},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.703944742679596},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.697212815284729},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6527644991874695},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6361286640167236},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5207021832466125},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4353010654449463},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.3172767162322998},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.1687493622303009},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14975261688232422},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1076706051826477},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10547125339508057}],"concepts":[{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.8326138257980347},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.7168453931808472},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.703944742679596},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.697212815284729},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6527644991874695},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6361286640167236},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5207021832466125},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4353010654449463},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.3172767162322998},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.1687493622303009},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14975261688232422},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1076706051826477},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10547125339508057},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/fpl.2007.4380764","is_oa":false,"landing_page_url":"https://doi.org/10.1109/fpl.2007.4380764","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 International Conference on Field Programmable Logic and Applications","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.396.120","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.396.120","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.ccrc.wustl.edu/~roger/papers/hjlbc07.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.545.7419","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.545.7419","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://hpcb.wustl.edu/pubs/fpl07.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1659313070","https://openalex.org/W2027266885","https://openalex.org/W2060022314","https://openalex.org/W2072763119","https://openalex.org/W2087064593","https://openalex.org/W2115303170","https://openalex.org/W2133008414","https://openalex.org/W2142574874","https://openalex.org/W2143180875","https://openalex.org/W2144745211","https://openalex.org/W2158714788","https://openalex.org/W3150677990","https://openalex.org/W6665446346","https://openalex.org/W6668594571"],"related_works":["https://openalex.org/W2891987081","https://openalex.org/W2317245370","https://openalex.org/W4249323025","https://openalex.org/W198851386","https://openalex.org/W2030310580","https://openalex.org/W947442053","https://openalex.org/W2148915962","https://openalex.org/W2283866686","https://openalex.org/W27867058","https://openalex.org/W1980160788"],"abstract_inverted_index":{"Large-scale":[0],"protein":[1],"sequence":[2],"comparison":[3],"is":[4,34],"an":[5,52],"important":[6],"but":[7],"compute-intensive":[8],"task":[9,19],"in":[10,66],"molecular":[11],"biology.":[12],"The":[13],"popular":[14],"BLASTP":[15,74,80,87],"software":[16,86],"for":[17,24,49],"this":[18,31],"has":[20,63],"become":[21],"a":[22,45,89],"bottleneck":[23],"proteomic":[25],"database":[26],"search.":[27],"One":[28],"third":[29],"of":[30,59,72],"software's":[32],"time":[33],"spent":[35],"executing":[36],"the":[37,57,73],"Smith-Waterman":[38],"dynamic":[39],"programming":[40],"algorithm.":[41,75],"This":[42,61],"work":[43],"describes":[44],"novel":[46],"FPGA":[47],"design":[48,62],"banded":[50],"Smith-Waterman,":[51],"algorithmic":[53],"variant":[54],"tuned":[55],"to":[56],"needs":[58],"BLASTP.":[60],"been":[64],"implemented":[65],"Mercury":[67,79],"BLASTP,":[68],"our":[69],"FPGA-accelerated":[70],"version":[71],"We":[76],"show":[77],"that":[78],"runs":[81],"6-16":[82],"times":[83],"faster":[84],"than":[85],"on":[88],"modern":[90],"CPU":[91],"while":[92],"delivering":[93],"99%":[94],"identical":[95],"results.":[96]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":4}],"updated_date":"2026-03-06T13:50:29.536080","created_date":"2025-10-10T00:00:00"}
