{"id":"https://openalex.org/W2059848742","doi":"https://doi.org/10.1145/1183401.1183442","title":"Accelerator design for protein sequence HMM search","display_name":"Accelerator design for protein sequence HMM search","publication_year":2006,"publication_date":"2006-06-28","ids":{"openalex":"https://openalex.org/W2059848742","doi":"https://doi.org/10.1145/1183401.1183442","mag":"2059848742"},"language":"en","primary_location":{"id":"doi:10.1145/1183401.1183442","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1183401.1183442","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 20th annual 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/A5073711744","display_name":"Rahul Pratap Maddimsetty","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":"Rahul P. Maddimsetty","raw_affiliation_strings":["Washington University, St. Louis, MO","Washington University, St. Louis, Mo"],"affiliations":[{"raw_affiliation_string":"Washington University, St. Louis, MO","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Washington University, St. Louis, Mo","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":["Washington University, St. Louis, MO","Washington University, St. Louis, Mo"],"affiliations":[{"raw_affiliation_string":"Washington University, St. Louis, MO","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Washington University, St. Louis, Mo","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","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":["Washington University, St. Louis, MO","Washington University, St. Louis, Mo"],"affiliations":[{"raw_affiliation_string":"Washington University, St. Louis, MO","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Washington University, St. Louis, Mo","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103563859","display_name":"Mark A. Franklin","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":"Mark A. Franklin","raw_affiliation_strings":["Washington University, St. Louis, MO","Washington University, St. Louis, Mo"],"affiliations":[{"raw_affiliation_string":"Washington University, St. Louis, MO","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Washington University, St. Louis, Mo","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"last","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":false,"raw_author_name":"Brandon Harris","raw_affiliation_strings":["Washington University, St. Louis, MO","Washington University, St. Louis, Mo"],"affiliations":[{"raw_affiliation_string":"Washington University, St. Louis, MO","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Washington University, St. Louis, Mo","institution_ids":["https://openalex.org/I204465549"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5073711744"],"corresponding_institution_ids":["https://openalex.org/I204465549"],"apc_list":null,"apc_paid":null,"fwci":9.0364,"has_fulltext":false,"cited_by_count":47,"citation_normalized_percentile":{"value":0.97728293,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"288","last_page":"296"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9969000220298767,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.991100013256073,"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":0.8039374947547913},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7980287075042725},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7424570918083191},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.658392608165741},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.63139408826828},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.6282528638839722},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5029086470603943},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2625262141227722},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20141929388046265},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09697514772415161}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8039374947547913},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7980287075042725},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7424570918083191},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.658392608165741},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.63139408826828},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.6282528638839722},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5029086470603943},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2625262141227722},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20141929388046265},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09697514772415161}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1183401.1183442","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1183401.1183442","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 20th annual international conference on Supercomputing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W180566773","https://openalex.org/W1598336441","https://openalex.org/W1608326296","https://openalex.org/W1986409054","https://openalex.org/W2023226967","https://openalex.org/W2072763119","https://openalex.org/W2087064593","https://openalex.org/W2094519647","https://openalex.org/W2097555181","https://openalex.org/W2102122585","https://openalex.org/W2102941975","https://openalex.org/W2125838338","https://openalex.org/W2130212247","https://openalex.org/W2141885858","https://openalex.org/W2142574874","https://openalex.org/W2148853951","https://openalex.org/W2166045208","https://openalex.org/W3214380909","https://openalex.org/W4210400672","https://openalex.org/W4245668478","https://openalex.org/W6607343744","https://openalex.org/W6668594571"],"related_works":["https://openalex.org/W2317245370","https://openalex.org/W4249323025","https://openalex.org/W198851386","https://openalex.org/W2030310580","https://openalex.org/W947442053","https://openalex.org/W1980160788","https://openalex.org/W2148915962","https://openalex.org/W2283866686","https://openalex.org/W4287182096","https://openalex.org/W27867058"],"abstract_inverted_index":{"Profile":[0],"Hidden":[1],"Markov":[2],"models":[3,24,175],"(HMMs)":[4],"are":[5,25,126,176,202],"a":[6,75,86,104,153,189],"powerful":[7],"approach":[8,169],"to":[9,28,33,51,157,178,188,197],"describing":[10],"biologically":[11],"significant":[12,109],"functional":[13],"units,":[14],"or":[15],"motifs,":[16],"in":[17,36,53,74],"protein":[18,47],"sequences.":[19],"Entire":[20],"databases":[21,50],"of":[22,31,41,62,77,116,121,132,137,148,155,164,195,200],"such":[23],"regularly":[26],"compared":[27],"large":[29],"collections":[30],"proteins":[32],"recognize":[34],"motifs":[35],"them.":[37],"Exponentially":[38],"increasing":[39,129],"rates":[40],"genome":[42],"sequencing":[43],"have":[44],"caused":[45],"both":[46],"and":[48,160],"model":[49],"explode":[52],"size,":[54],"placing":[55],"an":[56,67],"ever-increasing":[57],"computational":[58],"burden":[59],"on":[60,103],"users":[61],"these":[63],"systems.Here,":[64],"we":[65],"describe":[66],"accelerated":[68],"search":[69],"system":[70],"that":[71,183],"exploits":[72],"parallelism":[73],"number":[76],"ways.":[78],"First,":[79],"the":[80,97,117,122,130,138,146,149,162,180],"application":[81],"is":[82,101,170],"functionally":[83],"decomposed":[84],"into":[85],"pipeline,":[87],"with":[88],"distinct":[89],"compute":[90],"resources":[91],"executing":[92],"each":[93,168],"pipeline":[94,99,124],"stage.":[95],"Second,":[96],"first":[98,123,139],"stage":[100,125,140],"deployed":[102],"systolic":[105],"array,":[106],"which":[107,167],"yields":[108],"fine-grained":[110],"parallelism.":[111],"Third,":[112],"for":[113,145],"some":[114],"instantiations":[115],"design,":[118],"parallel":[119],"copies":[120],"used,":[127],"further":[128],"level":[131],"coarse-grained":[133],"parallelism.A":[134],"na\u00efve":[135],"parallelization":[136],"computation":[141],"has":[142],"serious":[143],"repercussions":[144],"sensitivity":[147],"search.":[150],"We":[151],"present":[152],"pair":[154],"remedies":[156],"this":[158],"dilemma":[159],"quantify":[161],"regions":[163],"interest":[165],"within":[166],"most":[171],"effective.":[172],"Analytic":[173],"performance":[174],"used":[177],"assess":[179],"overall":[181],"speedup":[182],"can":[184],"be":[185],"attained":[186],"relative":[187],"single-processor":[190],"software":[191],"solution.":[192],"Performance":[193],"improvements":[194],"1":[196],"2":[198],"orders":[199],"magnitude":[201],"predicted.":[203]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"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"}
