{"id":"https://openalex.org/W2047552440","doi":"https://doi.org/10.1145/2435264.2435329","title":"Acceleration of the long read mapping on a PC-FPGA architecture (abstract only)","display_name":"Acceleration of the long read mapping on a PC-FPGA architecture (abstract only)","publication_year":2013,"publication_date":"2013-02-11","ids":{"openalex":"https://openalex.org/W2047552440","doi":"https://doi.org/10.1145/2435264.2435329","mag":"2047552440"},"language":"en","primary_location":{"id":"doi:10.1145/2435264.2435329","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2435264.2435329","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM/SIGDA international symposium on Field programmable gate arrays","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/A5101837714","display_name":"Peng Chen","orcid":"https://orcid.org/0000-0001-9021-021X"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Peng Chen","raw_affiliation_strings":["University of Sciense and Technology of China, HeFei, China"],"affiliations":[{"raw_affiliation_string":"University of Sciense and Technology of China, HeFei, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011884768","display_name":"Chao Wang","orcid":"https://orcid.org/0000-0002-9403-5575"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chao Wang","raw_affiliation_strings":["University of Sciense and Technology of China, HeFei, China"],"affiliations":[{"raw_affiliation_string":"University of Sciense and Technology of China, HeFei, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100407749","display_name":"Xi Li","orcid":"https://orcid.org/0009-0003-7871-5401"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xi Li","raw_affiliation_strings":["University of Sciense and Technology of China, HeFei, China"],"affiliations":[{"raw_affiliation_string":"University of Sciense and Technology of China, HeFei, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077322091","display_name":"Xuehai Zhou","orcid":"https://orcid.org/0000-0002-8360-3143"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuehai Zhou","raw_affiliation_strings":["University of Sciense and Technology of China, HeFei, China"],"affiliations":[{"raw_affiliation_string":"University of Sciense and Technology of China, HeFei, China","institution_ids":["https://openalex.org/I126520041"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101837714"],"corresponding_institution_ids":["https://openalex.org/I126520041"],"apc_list":null,"apc_paid":null,"fwci":0.4386,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.64775,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"271","last_page":"271"},"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":0.9919000267982483,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9825000166893005,"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/bottleneck","display_name":"Bottleneck","score":0.8260565400123596},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7911319732666016},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.694408118724823},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.5009386539459229},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.49664026498794556},{"id":"https://openalex.org/keywords/ranging","display_name":"Ranging","score":0.48931190371513367},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.4666483402252197},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.43873330950737},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.42083340883255005},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.40599071979522705},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.2787052094936371},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.27068614959716797},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.20455193519592285},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07688936591148376},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.07402652502059937}],"concepts":[{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.8260565400123596},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7911319732666016},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.694408118724823},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.5009386539459229},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.49664026498794556},{"id":"https://openalex.org/C115051666","wikidata":"https://www.wikidata.org/wiki/Q6522493","display_name":"Ranging","level":2,"score":0.48931190371513367},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.4666483402252197},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.43873330950737},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.42083340883255005},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.40599071979522705},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.2787052094936371},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.27068614959716797},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.20455193519592285},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07688936591148376},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.07402652502059937},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2435264.2435329","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2435264.2435329","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM/SIGDA international symposium on Field programmable gate arrays","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","score":0.5400000214576721,"display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1977512185","https://openalex.org/W2013733655","https://openalex.org/W2037113830","https://openalex.org/W2055043387","https://openalex.org/W2062444839","https://openalex.org/W2072193858","https://openalex.org/W2080038972","https://openalex.org/W2103441770","https://openalex.org/W2106678197","https://openalex.org/W2107282968","https://openalex.org/W2111305378","https://openalex.org/W2115872073","https://openalex.org/W2121762798","https://openalex.org/W2124985265","https://openalex.org/W2136145671","https://openalex.org/W2139760555","https://openalex.org/W2141978878","https://openalex.org/W2143124024","https://openalex.org/W2146496959","https://openalex.org/W2150356570","https://openalex.org/W2153527981","https://openalex.org/W2154826966","https://openalex.org/W2156976066","https://openalex.org/W2166621589","https://openalex.org/W2171071054","https://openalex.org/W4247053599"],"related_works":["https://openalex.org/W2783354812","https://openalex.org/W4384112194","https://openalex.org/W2103009189","https://openalex.org/W4312958259","https://openalex.org/W4308259661","https://openalex.org/W4390813131","https://openalex.org/W2349383066","https://openalex.org/W4328132048","https://openalex.org/W1969901537","https://openalex.org/W2119768059"],"abstract_inverted_index":{"The":[0,128],"genome":[1,45,62],"sequence":[2,8],"alignment,":[3],"whereby":[4],"ultra":[5],"scale":[6],"of":[7,44,80,107,123,142,154],"reads":[9,42,63,177],"should":[10],"be":[11],"compared":[12],"to":[13,23,39,119,183],"an":[14],"enormous":[15],"long":[16,28,61,97,125],"reference,":[17],"has":[18,57],"been":[19,58],"one":[20],"central":[21],"challenge":[22],"the":[24,52,72,75,81,91,105,121,124,134,140,143,159,166],"biologists":[25],"for":[26,51,90,176],"a":[27,114,149],"period.":[29],"For":[30],"recent":[31],"years,":[32],"new":[33],"sequencing":[34],"technology":[35],"makes":[36],"it":[37,175],"possible":[38],"generate":[40],"longer":[41,65],"(sequences":[43],"fragments)":[46],"which":[47],"seem":[48],"more":[49],"valuable":[50],"life":[53],"science":[54],"research.":[55],"It":[56],"foreseen":[59],"that":[60,158],"(length":[64],"than":[66,174],"200":[67],"base":[68],"pairs)":[69],"will":[70],"dominate":[71],"field":[73],"in":[74,152],"near":[76],"future.":[77],"Unfortunately,":[78],"most":[79],"state-of-art":[82],"aligners":[83,99],"nowadays":[84],"are":[85,100],"optimized":[86],"and":[87,137,169],"only":[88],"applicable":[89],"short":[92],"read":[93,98,126],"mapping":[94],"while":[95],"present":[96],"still":[101],"not":[102],"satisfying":[103],"at":[104],"aspect":[106],"speed.":[108,155],"In":[109],"this":[110],"paper,":[111],"we":[112],"propose":[113],"novel":[115],"PC-FPGA":[116],"hybrid":[117],"system":[118,161],"improve":[120],"performance":[122],"mapping.":[127],"BWA-SW":[129,167],"algorithm":[130],"is":[131,162],"chosen":[132],"as":[133,163,165],"alignment":[135],"approach":[136],"by":[138],"accelerating":[139],"bottleneck":[141],"algorithm,":[144],"our":[145],"solution":[146],"could":[147],"archive":[148],"significant":[150],"improvement":[151],"term":[153],"Experiments":[156],"demonstrate":[157],"described":[160],"accurate":[164],"aligner":[168],"about":[170],"1.41-2.73":[171],"times":[172],"faster":[173],"with":[178],"lengths":[179],"ranging":[180],"from":[181],"500bp":[182],"2000bp.":[184]},"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
