{"id":"https://openalex.org/W2057496513","doi":"https://doi.org/10.1145/1810085.1810099","title":"Fast and accurate NCBI BLASTP","display_name":"Fast and accurate NCBI BLASTP","publication_year":2010,"publication_date":"2010-06-02","ids":{"openalex":"https://openalex.org/W2057496513","doi":"https://doi.org/10.1145/1810085.1810099","mag":"2057496513"},"language":"en","primary_location":{"id":"doi:10.1145/1810085.1810099","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1810085.1810099","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 24th ACM International Conference on Supercomputing","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/A5048458032","display_name":"Atabak Mahram","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Atabak Mahram","raw_affiliation_strings":["Boston University, Boston, MA"],"affiliations":[{"raw_affiliation_string":"Boston University, Boston, MA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021051610","display_name":"Martin Herbordt","orcid":"https://orcid.org/0000-0002-3443-9113"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Martin C. Herbordt","raw_affiliation_strings":["Boston University, Boston, MA"],"affiliations":[{"raw_affiliation_string":"Boston University, Boston, MA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5048458032"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.1895,"has_fulltext":false,"cited_by_count":57,"citation_normalized_percentile":{"value":0.77290473,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"73","last_page":"82"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"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":0.9990000128746033,"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":0.998199999332428,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9751999974250793,"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":0.7617632150650024},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.7545164823532104},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.6605736017227173},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.6164795160293579},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5639594197273254},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.4769929051399231},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.46013444662094116},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.457175076007843},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.42228594422340393},{"id":"https://openalex.org/keywords/computer-engineering","display_name":"Computer engineering","score":0.36995527148246765},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.34403398633003235},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.24057331681251526},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14494627714157104},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07859805226325989},{"id":"https://openalex.org/keywords/electronic-engineering","display_name":"Electronic engineering","score":0.07413169741630554}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7617632150650024},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.7545164823532104},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.6605736017227173},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.6164795160293579},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5639594197273254},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.4769929051399231},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.46013444662094116},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.457175076007843},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.42228594422340393},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.36995527148246765},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.34403398633003235},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.24057331681251526},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14494627714157104},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07859805226325989},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.07413169741630554},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1810085.1810099","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1810085.1810099","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 24th ACM International Conference on Supercomputing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4575648291","display_name":null,"funder_award_id":"R01-RR023168-01A1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1716835390","https://openalex.org/W1757537413","https://openalex.org/W1864817015","https://openalex.org/W1978885894","https://openalex.org/W1981644820","https://openalex.org/W2012189243","https://openalex.org/W2026029521","https://openalex.org/W2043198910","https://openalex.org/W2055043387","https://openalex.org/W2103148772","https://openalex.org/W2103644816","https://openalex.org/W2125062675","https://openalex.org/W2125369168","https://openalex.org/W2129713651","https://openalex.org/W2133098231","https://openalex.org/W2143180875","https://openalex.org/W2156264615","https://openalex.org/W2159224090","https://openalex.org/W2163764537","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2280422768","https://openalex.org/W3143197806","https://openalex.org/W4252555497","https://openalex.org/W3121175838","https://openalex.org/W3016293053","https://openalex.org/W2401723157","https://openalex.org/W2952904874","https://openalex.org/W324626582","https://openalex.org/W4389302559","https://openalex.org/W1690653314"],"abstract_inverted_index":{"NCBI":[0,147],"BLAST":[1],"has":[2],"become":[3],"the":[4,43,66,83,107,120,130,134,162],"de":[5],"facto":[6],"standard":[7,96],"in":[8,156],"bioinformatic":[9],"approximate":[10],"string":[11],"matching":[12],"and":[13,39,133,137,151],"so":[14],"its":[15],"acceleration":[16],"is":[17,23,79,101,113,152],"of":[18,73,104,116],"fundamental":[19],"importance.":[20],"The":[21,75,99],"problem":[22],"that":[24,55],"it":[25,31],"uses":[26],"complex":[27],"heuristics":[28],"which":[29,111],"make":[30],"difficult":[32],"to":[33,64,80],"simultaneously":[34],"achieve":[35],"both":[36,129],"substantial":[37],"speed-up":[38],"exact":[40],"agreement":[41],"with":[42,89],"original":[44,131],"output.":[45],"We":[46],"have":[47],"previously":[48],"described":[49],"how":[50,82],"a":[51,102],"novel":[52],"FPGA-based":[53,158],"prefilter":[54],"performs":[56],"exhaustive":[57],"ungapped":[58],"alignment":[59],"(EUA)":[60],"could":[61],"be":[62,87],"used":[63],"reduce":[65],"computation":[67],"by":[68],"over":[69,106],"99.9%":[70],"without":[71],"loss":[72],"sensitivity.":[74],"primary":[76],"contribution":[77],"here":[78],"show":[81],"EUA":[84,132],"filter":[85],"can":[86],"combined":[88],"another":[90],"filter,":[91],"this":[92],"one":[93],"based":[94],"on":[95],"2-hit":[97,135],"seeding.":[98],"result":[100],"doubling":[103],"performance":[105],"previous":[108],"best":[109],"implementation,":[110],"itself":[112],"an":[114],"order":[115],"magnitude":[117],"faster":[118],"than":[119],"unaccelerated":[121],"original.":[122],"Other":[123],"contributions":[124],"include":[125],"new":[126,144],"algorithms":[127],"for":[128,154],"filters":[136],"experimental":[138],"results":[139],"demonstrating":[140],"their":[141],"utility.":[142],"This":[143],"multiphase":[145],"FPGA-accelerated":[146],"BLASTP":[148],"scales":[149],"easily":[150],"appropriate":[153],"use":[155],"large":[157],"servers":[159],"such":[160],"as":[161],"Novo-G.":[163]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
