{"id":"https://openalex.org/W2019628919","doi":"https://doi.org/10.1145/2016741.2016772","title":"Autotuned parallel I/O for highly scalable biosequence analysis","display_name":"Autotuned parallel I/O for highly scalable biosequence analysis","publication_year":2011,"publication_date":"2011-07-18","ids":{"openalex":"https://openalex.org/W2019628919","doi":"https://doi.org/10.1145/2016741.2016772","mag":"2019628919"},"language":"en","primary_location":{"id":"doi:10.1145/2016741.2016772","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2016741.2016772","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery","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/A5017918038","display_name":"Haihang You","orcid":"https://orcid.org/0000-0003-1432-827X"},"institutions":[{"id":"https://openalex.org/I4210159558","display_name":"Joint Institute for Computational Sciences","ror":"https://ror.org/05277x335","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294","https://openalex.org/I4210159558","https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haihang You","raw_affiliation_strings":["National Institute for Computational Science, Oak Ridge, TN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute for Computational Science, Oak Ridge, TN","institution_ids":["https://openalex.org/I4210159558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033799238","display_name":"Bhanu Rekapalli","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159558","display_name":"Joint Institute for Computational Sciences","ror":"https://ror.org/05277x335","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294","https://openalex.org/I4210159558","https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bhanu Rekapalli","raw_affiliation_strings":["National Institute for Computational Science, Oak Ridge, TN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute for Computational Science, Oak Ridge, TN","institution_ids":["https://openalex.org/I4210159558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100345219","display_name":"Qing Liu","orcid":"https://orcid.org/0000-0002-7600-7976"},"institutions":[{"id":"https://openalex.org/I4210159558","display_name":"Joint Institute for Computational Sciences","ror":"https://ror.org/05277x335","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294","https://openalex.org/I4210159558","https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qing Liu","raw_affiliation_strings":["National Institute for Computational Science, Oak Ridge, TN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute for Computational Science, Oak Ridge, TN","institution_ids":["https://openalex.org/I4210159558"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041037945","display_name":"Shirley Moore","orcid":"https://orcid.org/0009-0009-1351-2797"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shirley Moore","raw_affiliation_strings":["University of Tennessee, Knoxville, TN","University of Tennessee, Knoxville, TN;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Tennessee, Knoxville, TN","institution_ids":["https://openalex.org/I75027704"]},{"raw_affiliation_string":"University of Tennessee, Knoxville, TN;","institution_ids":["https://openalex.org/I75027704"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4396,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.72469712,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9997000098228455,"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":0.9997000098228455,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9976000189781189,"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"}},{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/scalability","display_name":"Scalability","score":0.8003918528556824},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7877241373062134},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6918262243270874},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.6566999554634094},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.644540011882782},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5817148089408875},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5695803165435791},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.542949914932251},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5143450498580933},{"id":"https://openalex.org/keywords/parallel-processing","display_name":"Parallel processing","score":0.47534653544425964},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3659101724624634},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.15956366062164307},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1370866596698761},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11215084791183472}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.8003918528556824},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7877241373062134},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6918262243270874},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.6566999554634094},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.644540011882782},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5817148089408875},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5695803165435791},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.542949914932251},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5143450498580933},{"id":"https://openalex.org/C106515295","wikidata":"https://www.wikidata.org/wiki/Q26806595","display_name":"Parallel processing","level":2,"score":0.47534653544425964},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3659101724624634},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.15956366062164307},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1370866596698761},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11215084791183472},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2016741.2016772","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2016741.2016772","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.659.2304","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.659.2304","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://icl.cs.utk.edu/news_pub/submissions/hmmer.pdf?origin%3Dpublication_detail","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2210822915","display_name":null,"funder_award_id":"EPS-0919436","funder_id":"https://openalex.org/F4320338283","funder_display_name":"Office of Experimental Program to Stimulate Competitive Research"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320338283","display_name":"Office of Experimental Program to Stimulate Competitive Research","ror":"https://ror.org/04k9mqs78"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1589918049","https://openalex.org/W1598336441","https://openalex.org/W1964031104","https://openalex.org/W1968400011","https://openalex.org/W1972209410","https://openalex.org/W2039765803","https://openalex.org/W2058797440","https://openalex.org/W2059848742","https://openalex.org/W2060171832","https://openalex.org/W2096070062","https://openalex.org/W2130212247","https://openalex.org/W2136440628","https://openalex.org/W2136874833","https://openalex.org/W2141885858","https://openalex.org/W2148542244","https://openalex.org/W2151831732","https://openalex.org/W4236611442","https://openalex.org/W4243796884","https://openalex.org/W6660493486","https://openalex.org/W6681765588"],"related_works":["https://openalex.org/W2056543843","https://openalex.org/W2073684863","https://openalex.org/W2172228568","https://openalex.org/W2234221250","https://openalex.org/W1624166738","https://openalex.org/W1943306263","https://openalex.org/W2371903265","https://openalex.org/W2102735377","https://openalex.org/W2154741861","https://openalex.org/W2090758225"],"abstract_inverted_index":{"In":[0,95],"recent":[1],"years,":[2],"the":[3,16,33,41,45,71,84,139],"rate":[4,27],"of":[5,47,52,75,104,132,142,144,151],"genomics":[6,20,90],"sequence":[7,55],"generation":[8],"increased":[9],"dramatically":[10],"due":[11],"to":[12,86],"significant":[13],"advances":[14],"in":[15,28,44,83,146],"sequencing":[17],"technology.":[18],"The":[19],"data":[21,91],"is":[22],"accumulating":[23],"at":[24],"an":[25,100],"exponential":[26],"various":[29],"databases":[30,56],"all":[31],"around":[32],"world":[34],"and":[35,49,73],"rapid":[36],"analysis":[37],"techniques":[38],"will":[39],"enhance":[40],"knowledge":[42],"discovery":[43],"fields":[46],"medicine":[48],"biotechnology.":[50],"Analysis":[51],"such":[53],"growing":[54],"demands":[57],"tremendous":[58],"computational":[59],"power":[60],"that":[61],"can":[62],"only":[63],"be":[64],"provided":[65],"by":[66],"massively":[67],"parallel":[68,102,121],"computers.":[69],"Improving":[70],"performance":[72],"scalability":[74],"bioinformatics":[76],"tools":[77],"thus":[78],"becomes":[79],"a":[80,105,136],"critical":[81],"step":[82],"quest":[85],"transform":[87],"ever-growing":[88],"raw":[89],"into":[92],"biological":[93],"knowledge.":[94],"this":[96],"paper":[97],"we":[98],"describe":[99],"efficient":[101],"implementation":[103],"profile":[106],"hidden":[107],"Markov":[108],"models":[109],"(profile":[110],"HMMs)":[111],"code":[112],"used":[113],"for":[114],"protein":[115],"domain":[116,140],"identification,":[117],"along":[118],"with":[119,129],"auto-tuned":[120],"I/O":[122],"optimization.":[123],"Experimental":[124],"results":[125],"show":[126],"linear":[127],"speedup":[128],"increasing":[130],"numbers":[131],"computing":[133,153],"cores":[134],"on":[135],"supercomputer,":[137],"allowing":[138],"identification":[141],"millions":[143],"proteins":[145],"few":[147],"minutes":[148],"using":[149],"hundreds":[150],"thousands":[152],"cores.":[154]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
