{"id":"https://openalex.org/W2159224090","doi":"https://doi.org/10.1109/fccm.2009.27","title":"CAAD BLASTP: NCBI BLASTP Accelerated with FPGA-Based Accelerated Pre-Filtering","display_name":"CAAD BLASTP: NCBI BLASTP Accelerated with FPGA-Based Accelerated Pre-Filtering","publication_year":2009,"publication_date":"2009-01-01","ids":{"openalex":"https://openalex.org/W2159224090","doi":"https://doi.org/10.1109/fccm.2009.27","mag":"2159224090"},"language":"en","primary_location":{"id":"doi:10.1109/fccm.2009.27","is_oa":false,"landing_page_url":"https://doi.org/10.1109/fccm.2009.27","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 17th IEEE Symposium on Field Programmable Custom Computing Machines","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/A5103048363","display_name":"Jin H. Park","orcid":"https://orcid.org/0000-0001-7017-4979"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jin H. Park","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000342843","display_name":"Yunfei Qiu","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yunfei Qiu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021051610","display_name":"Martin Herbordt","orcid":"https://orcid.org/0000-0002-3443-9113"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin C. Herbordt","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I111088046"],"apc_list":null,"apc_paid":null,"fwci":1.2185,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.8080088,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"48","issue":null,"first_page":"81","last_page":"87"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9990000128746033,"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":0.9990000128746033,"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":0.9973999857902527,"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/T12326","display_name":"Network Packet Processing and Optimization","score":0.9754999876022339,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.769523024559021},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7633498907089233},{"id":"https://openalex.org/keywords/append","display_name":"Append","score":0.7174949645996094},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.6894183158874512},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.6758139133453369},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.6545963287353516},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5390152335166931},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.5165006518363953},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.49048611521720886},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.4565763473510742},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.42673003673553467},{"id":"https://openalex.org/keywords/timeline","display_name":"Timeline","score":0.425375372171402},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27845299243927},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.2265150249004364},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.2156536877155304},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08823859691619873},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.08384168148040771},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08356162905693054},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07738381624221802},{"id":"https://openalex.org/keywords/electronic-engineering","display_name":"Electronic engineering","score":0.07557642459869385}],"concepts":[{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.769523024559021},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7633498907089233},{"id":"https://openalex.org/C2777998813","wikidata":"https://www.wikidata.org/wiki/Q16869124","display_name":"Append","level":2,"score":0.7174949645996094},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.6894183158874512},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.6758139133453369},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.6545963287353516},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5390152335166931},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.5165006518363953},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.49048611521720886},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.4565763473510742},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.42673003673553467},{"id":"https://openalex.org/C4438859","wikidata":"https://www.wikidata.org/wiki/Q186117","display_name":"Timeline","level":2,"score":0.425375372171402},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27845299243927},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.2265150249004364},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.2156536877155304},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08823859691619873},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.08384168148040771},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08356162905693054},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07738381624221802},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.07557642459869385},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/fccm.2009.27","is_oa":false,"landing_page_url":"https://doi.org/10.1109/fccm.2009.27","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2009 17th IEEE Symposium on Field Programmable Custom Computing Machines","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":13,"referenced_works":["https://openalex.org/W1608326296","https://openalex.org/W1978885894","https://openalex.org/W1981644820","https://openalex.org/W2012189243","https://openalex.org/W2043198910","https://openalex.org/W2043530994","https://openalex.org/W2055043387","https://openalex.org/W2133098231","https://openalex.org/W2142574874","https://openalex.org/W2143180875","https://openalex.org/W2163764537","https://openalex.org/W4236236547","https://openalex.org/W4246147816"],"related_works":["https://openalex.org/W1858249912","https://openalex.org/W2114034199","https://openalex.org/W4391249598","https://openalex.org/W2317428717","https://openalex.org/W2734259032","https://openalex.org/W3094038556","https://openalex.org/W2014772881","https://openalex.org/W4254228154","https://openalex.org/W3049477255","https://openalex.org/W4296345146"],"abstract_inverted_index":{"NCBI":[0,115,137],"BLAST":[1,127],"has":[2],"become":[3],"the":[4,43,51,80,89],"de":[5],"facto":[6],"standard":[7],"in":[8],"bioinformatic":[9],"approximate":[10],"string":[11],"matching":[12],"and":[13,39,86,91,129],"so":[14],"its":[15],"acceleration":[16],"is":[17,23,48,123],"of":[18,84,107,112,118],"fundamental":[19],"importance.":[20],"The":[21],"problem":[22],"that":[24],"it":[25,31],"uses":[26],"complex":[27],"heuristics":[28],"which":[29,63],"make":[30,54],"difficult":[32],"to":[33,49,66,77,125],"simultaneously":[34],"achieve":[35],"both":[36],"substantial":[37],"speed-up":[38,106],"exact":[40],"agreement":[41],"with":[42],"original":[44],"output.":[45],"Our":[46],"approach":[47],"prefilter":[50],"database.":[52],"To":[53],"this":[55],"work":[56],"we":[57,64,103],"have":[58],"developed":[59],"a":[60,67,105,110],"novel":[61],"heuristic":[62],"append":[65],"previously":[68],"described":[69],"structure":[70],"for":[71,88,114],"ungapped":[72,90],"alignment.":[73],"This":[74,121],"enables":[75],"us":[76],"quickly":[78],"reduce":[79],"database":[81],"by":[82],"factors":[83],"300":[85],"1100,":[87],"gapped":[92],"options,":[93],"respectively,":[94],"while":[95],"rejecting":[96],"no":[97],"significant":[98],"sequences.":[99],"On":[100],"current":[101],"hardware":[102],"anticipate":[104],"at":[108],"least":[109],"factor":[111],"10":[113],"BLASTP,":[116],"independent":[117],"sensitivity":[119],"settings.":[120],"filter":[122],"portable":[124],"other":[126,130],"codes,":[128],"filters":[131],"can":[132],"be":[133],"similarly":[134],"integrated":[135],"into":[136],"BLAST.":[138]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
