{"id":"https://openalex.org/W1979068219","doi":"https://doi.org/10.1109/hpcsim.2014.6903731","title":"Optimized ASIP architecture for compressed BWT-indexed search in bioinformatics applications","display_name":"Optimized ASIP architecture for compressed BWT-indexed search in bioinformatics applications","publication_year":2014,"publication_date":"2014-07-01","ids":{"openalex":"https://openalex.org/W1979068219","doi":"https://doi.org/10.1109/hpcsim.2014.6903731","mag":"1979068219"},"language":"en","primary_location":{"id":"doi:10.1109/hpcsim.2014.6903731","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpcsim.2014.6903731","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 International Conference on High Performance Computing &amp; Simulation (HPCS)","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/A5038468355","display_name":"Nuno Sebastio","orcid":null},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Nuno Sebastio","raw_affiliation_strings":["INESC-ID Instituto Superior T\u00e9cnico Universidade de Lisboa, Lisboa, Portugal","Inesc-ID"],"affiliations":[{"raw_affiliation_string":"INESC-ID Instituto Superior T\u00e9cnico Universidade de Lisboa, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]},{"raw_affiliation_string":"Inesc-ID","institution_ids":["https://openalex.org/I121345201"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002334825","display_name":"Paulo Flores","orcid":"https://orcid.org/0000-0003-2970-3589"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Paulo Flores","raw_affiliation_strings":["INESC-ID Instituto Superior T\u00e9cnico Universidade de Lisboa, Lisboa, Portugal","[INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol, 9, 1000-029 - Portugal]"],"affiliations":[{"raw_affiliation_string":"INESC-ID Instituto Superior T\u00e9cnico Universidade de Lisboa, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]},{"raw_affiliation_string":"[INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol, 9, 1000-029 - Portugal]","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015710714","display_name":"Nuno Roma","orcid":"https://orcid.org/0000-0003-2491-4977"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Nuno Roma","raw_affiliation_strings":["INESC-ID Instituto Superior T\u00e9cnico Universidade de Lisboa, Lisboa, Portugal","[INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol, 9, 1000-029 - Portugal]"],"affiliations":[{"raw_affiliation_string":"INESC-ID Instituto Superior T\u00e9cnico Universidade de Lisboa, Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]},{"raw_affiliation_string":"[INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Rua Alves Redol, 9, 1000-029 - Portugal]","institution_ids":["https://openalex.org/I141596103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5038468355"],"corresponding_institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"],"apc_list":null,"apc_paid":null,"fwci":0.409,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.72510713,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9936000108718872,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9904999732971191,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/microblaze","display_name":"MicroBlaze","score":0.8691664934158325},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8457353711128235},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7083209753036499},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.5916386842727661},{"id":"https://openalex.org/keywords/instruction-set","display_name":"Instruction set","score":0.5858522057533264},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.5454339981079102},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5083615183830261},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5079086422920227},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.49273136258125305},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.4527114927768707},{"id":"https://openalex.org/keywords/uncompressed-video","display_name":"Uncompressed video","score":0.4461723268032074},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3604907989501953},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.29560351371765137},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11837133765220642}],"concepts":[{"id":"https://openalex.org/C2777575374","wikidata":"https://www.wikidata.org/wiki/Q1644704","display_name":"MicroBlaze","level":3,"score":0.8691664934158325},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8457353711128235},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7083209753036499},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.5916386842727661},{"id":"https://openalex.org/C202491316","wikidata":"https://www.wikidata.org/wiki/Q272683","display_name":"Instruction set","level":2,"score":0.5858522057533264},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.5454339981079102},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5083615183830261},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5079086422920227},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.49273136258125305},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.4527114927768707},{"id":"https://openalex.org/C162478608","wikidata":"https://www.wikidata.org/wiki/Q4011369","display_name":"Uncompressed video","level":4,"score":0.4461723268032074},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3604907989501953},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.29560351371765137},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11837133765220642},{"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/C202474056","wikidata":"https://www.wikidata.org/wiki/Q1931635","display_name":"Video tracking","level":3,"score":0.0},{"id":"https://openalex.org/C65483669","wikidata":"https://www.wikidata.org/wiki/Q3536669","display_name":"Video processing","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/hpcsim.2014.6903731","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpcsim.2014.6903731","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 International Conference on High Performance Computing &amp; Simulation (HPCS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.4699999988079071}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W2059513841","https://openalex.org/W2101601013","https://openalex.org/W2103441770","https://openalex.org/W2124985265","https://openalex.org/W2126626169","https://openalex.org/W2129713651","https://openalex.org/W2132284451","https://openalex.org/W2154605789","https://openalex.org/W2158322625","https://openalex.org/W2161488606","https://openalex.org/W2162852139","https://openalex.org/W4256075606","https://openalex.org/W6679657429","https://openalex.org/W6684067881"],"related_works":["https://openalex.org/W2470589840","https://openalex.org/W2384714939","https://openalex.org/W2370911386","https://openalex.org/W1595151633","https://openalex.org/W1975010174","https://openalex.org/W1935885523","https://openalex.org/W1989119024","https://openalex.org/W3120511008","https://openalex.org/W2080419754","https://openalex.org/W39695077"],"abstract_inverted_index":{"Compressed":[0],"indexes":[1,41,62,111],"are":[2,63,76],"adopted":[3],"by":[4,36,66,165],"a":[5,67,124,157,173,193,199],"vast":[6],"set":[7],"of":[8,25,39,70,74,101,159,162,192,219,228,231],"bioinformatics":[9],"applications":[10],"that":[11,33],"deal":[12],"with":[13,54,133],"extremely":[14],"large":[15],"datasets,":[16],"mainly":[17],"due":[18],"to":[19,45,97,144,180,210],"the":[20,29,37,99,114,129,149,153,160,177,190,203,215,225],"inherently":[21],"high":[22],"memory":[23],"requirements":[24],"uncompressed":[26],"alternatives.":[27],"However,":[28],"additional":[30,134],"computational":[31,49],"overhead":[32],"is":[34,95],"imposed":[35],"usage":[38,69],"such":[40,51],"makes":[42],"them":[43],"harder":[44],"implement":[46],"in":[47,208],"embedded":[48],"platforms,":[50],"as":[52,214],"biochips,":[53],"strict":[55],"processing":[56,100,201,217,227],"and":[57,127,187],"power":[58],"restrictions.":[59],"Furthermore,":[60,169],"compressed":[61,109,140,151],"often":[64],"characterized":[65],"significant":[68],"bit-level":[71,135],"operations,":[72,136],"some":[73],"which":[75],"not":[77],"commonly":[78],"available":[79],"on":[80,113,172],"General":[81],"Purpose":[82],"Processors":[83],"(GPPs).":[84],"To":[85,197],"circumvent":[86],"this":[87],"limitation,":[88],"an":[89,182],"Application-Specific":[90],"Instruction-set":[91],"Processor":[92],"(ASIP)":[93],"architecture":[94,155],"proposed":[96,119,154,204],"accelerate":[98],"biological":[102,232],"sequences":[103],"(e.g.,":[104],"alignment,":[105],"mapping,":[106],"etc.)":[107],"using":[108],"full-text":[110],"based":[112],"Burrows-Wheeler":[115],"Transform":[116],"(BWT).":[117],"The":[118],"processor":[120],"was":[121,206],"built":[122],"over":[123,148],"RISC":[125],"micro-architecture":[126],"extends":[128],"Xilinx":[130,174],"MicroBlaze":[131],"ISA":[132],"especially":[137,222],"tailored":[138],"for":[139,189,224],"indexes.":[141],"When":[142],"used":[143,213],"perform":[145],"search":[146],"operations":[147],"considered":[150],"index,":[152],"provides":[156],"reduction":[158],"number":[161],"required":[163],"instructions":[164],"about":[166],"one":[167],"half.":[168],"when":[170],"prototyped":[171],"Virtex-7":[175],"FPGA,":[176],"ASIP":[178,205],"proved":[179],"offer":[181],"overall":[183],"speedup":[184],"between":[185],"3.1x":[186],"4.5x":[188],"execution":[191],"single":[194],"threaded":[195],"operation.":[196],"ensure":[198],"further":[200],"scalability,":[202],"designed":[207],"order":[209],"be":[211],"easily":[212],"basic":[216],"unit":[218],"multi-core":[220],"systems,":[221],"tuned":[223],"parallel":[226],"massive":[229],"datasets":[230],"reads.":[233]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
