{"id":"https://openalex.org/W2564249253","doi":"https://doi.org/10.1109/cibcb.2016.7758120","title":"FAST: Fast annotation with synchronized threads","display_name":"FAST: Fast annotation with synchronized threads","publication_year":2016,"publication_date":"2016-10-01","ids":{"openalex":"https://openalex.org/W2564249253","doi":"https://doi.org/10.1109/cibcb.2016.7758120","mag":"2564249253"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2016.7758120","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2016.7758120","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","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/A5000581119","display_name":"Dongjae Kim","orcid":"https://orcid.org/0000-0003-2871-7815"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Dongjae Kim","raw_affiliation_strings":["Department of Computer Science, University of British Columbia, Vancouver, BC, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055521337","display_name":"Aria S Hahn","orcid":"https://orcid.org/0000-0001-6105-7172"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Aria S. Hahn","raw_affiliation_strings":["Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada","Koonkie, Inc., Menlo Park, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"Koonkie, Inc., Menlo Park, CA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069094618","display_name":"Niels W. Hanson","orcid":"https://orcid.org/0000-0003-3081-0736"},"institutions":[{"id":"https://openalex.org/I4210155734","display_name":"KPMG (United States)","ror":"https://ror.org/049ngdd28","country_code":"US","type":"company","lineage":["https://openalex.org/I4210135825","https://openalex.org/I4210155734"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Niels W. Hanson","raw_affiliation_strings":["Data & Analytics, KPMG LLC, Seattle, WA, USA"],"affiliations":[{"raw_affiliation_string":"Data & Analytics, KPMG LLC, Seattle, WA, USA","institution_ids":["https://openalex.org/I4210155734"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035678865","display_name":"Kishori M. Konwar","orcid":"https://orcid.org/0000-0001-5152-4777"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kishori M. Konwar","raw_affiliation_strings":["Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA","Koonkie, Inc., Menlo Park, CA, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Koonkie, Inc., Menlo Park, CA, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101411528","display_name":"Steven Hallam","orcid":"https://orcid.org/0000-0002-4889-6876"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Steven J. Hallam","raw_affiliation_strings":["Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada","Koonkie, Inc., Menlo Park, CA, USA"],"affiliations":[{"raw_affiliation_string":"Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"Koonkie, Inc., Menlo Park, CA, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5000581119"],"corresponding_institution_ids":["https://openalex.org/I141945490"],"apc_list":null,"apc_paid":null,"fwci":0.5002,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.71699716,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"6","issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9987000226974487,"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":0.9890999794006348,"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":0.8506578207015991},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5687832832336426},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5521225333213806},{"id":"https://openalex.org/keywords/extensibility","display_name":"Extensibility","score":0.453387588262558},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.29513370990753174},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12445729970932007}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8506578207015991},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5687832832336426},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5521225333213806},{"id":"https://openalex.org/C32833848","wikidata":"https://www.wikidata.org/wiki/Q4115054","display_name":"Extensibility","level":2,"score":0.453387588262558},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.29513370990753174},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12445729970932007}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb.2016.7758120","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2016.7758120","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5600000023841858,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309949","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95"},{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320314000","display_name":"Compute Canada","ror":"https://ror.org/03ty8yr27"},{"id":"https://openalex.org/F4320319973","display_name":"Genome British Columbia","ror":"https://ror.org/03gne5057"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W57812598","https://openalex.org/W938539187","https://openalex.org/W1920637681","https://openalex.org/W1983572666","https://openalex.org/W1990061958","https://openalex.org/W1990092986","https://openalex.org/W2032574053","https://openalex.org/W2045204781","https://openalex.org/W2055043387","https://openalex.org/W2072970694","https://openalex.org/W2074906123","https://openalex.org/W2092574257","https://openalex.org/W2097892623","https://openalex.org/W2103441770","https://openalex.org/W2107903949","https://openalex.org/W2113561798","https://openalex.org/W2116895571","https://openalex.org/W2118750355","https://openalex.org/W2122210493","https://openalex.org/W2125826054","https://openalex.org/W2130564474","https://openalex.org/W2138122982","https://openalex.org/W2142428670","https://openalex.org/W2151831732","https://openalex.org/W2152420937","https://openalex.org/W2155606054","https://openalex.org/W2158874082","https://openalex.org/W2159482845","https://openalex.org/W2162473677","https://openalex.org/W2162481186","https://openalex.org/W2162758337","https://openalex.org/W2249344705","https://openalex.org/W4236236547","https://openalex.org/W4247053599","https://openalex.org/W4293763691","https://openalex.org/W4294216483","https://openalex.org/W6602299294","https://openalex.org/W6646522387"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W1948607442","https://openalex.org/W2361861616","https://openalex.org/W3004004161","https://openalex.org/W2044615423","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W4247766898","https://openalex.org/W2364420803"],"abstract_inverted_index":{"FAST":[0,9,88,113],"is":[1,10,76,115],"a":[2],"multi-threaded,":[3],"I/O":[4],"optimized":[5],"Seed-and-Extend":[6],"alignment":[7],"program.":[8],"extensible":[11],"to":[12,18,69,95],"nucleotide":[13],"sequences":[14,102],"making":[15],"it":[16],"comparable":[17],"both":[19],"BLASTn":[20],"and":[21,23,122],"BLASTp,":[22],"also":[24],"features":[25],"several":[26],"new":[27],"usage":[28],"flags":[29],"reporting":[30],"only":[31],"HSPs":[32],"meeting":[33],"user":[34],"defined":[35],"e-value":[36],"cut-offs.":[37],"FASTs":[38],"threaded":[39,62],"database":[40,46,63,91],"construction":[41,47,64,85,92],"allows":[42],"fast,":[43],"low":[44],"memory":[45],"e.g.,":[48],"RefSeq":[49],"(9.4GB)":[50],"can":[51,125],"be":[52,126],"indexed":[53],"in":[54],"under":[55],"5":[56],"minutes":[57],"using":[58],"20":[59],"threads.":[60],"The":[61,112],"gives":[65],"users":[66,94],"the":[67,105,109],"ability":[68],"create":[70],"custom":[71],"databases":[72,98],"on":[73,128],"demand":[74],"which":[75],"useful":[77],"for":[78],"tasks":[79],"requiring":[80],"self-alignment,":[81],"such":[82],"as":[83],"network":[84],"[30].":[86],"Finally,":[87],"supports":[89],"incremental":[90],"enabling":[93],"keep":[96],"their":[97],"up-to-date":[99],"by":[100],"adding":[101],"without":[103],"suffering":[104],"cost":[106],"of":[107],"reformatting":[108],"entire":[110],"database.":[111],"source":[114],"freely":[116],"available":[117],"through":[118],"GitHub":[119],"https://":[120],"github.com/hallamlab/FAST":[121],"test":[123],"datasets":[124],"found":[127],"Dropbox":[129],"https://www.dropbox.com/sh/xvvavweuzgqybc4/":[130],"AAAWCrRnol67ZsXi2qLQWUuOa?":[131]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}