{"id":"https://openalex.org/W3209783322","doi":"https://doi.org/10.1145/3458817.3476202","title":"FastZ","display_name":"FastZ","publication_year":2021,"publication_date":"2021-10-21","ids":{"openalex":"https://openalex.org/W3209783322","doi":"https://doi.org/10.1145/3458817.3476202","mag":"3209783322"},"language":"en","primary_location":{"id":"doi:10.1145/3458817.3476202","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3458817.3476202","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3458817.3476202","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3458817.3476202","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060960403","display_name":"Sree Charan Gundabolu","orcid":"https://orcid.org/0000-0001-6220-6926"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sree Charan Gundabolu","raw_affiliation_strings":["Purdue University"],"affiliations":[{"raw_affiliation_string":"Purdue University","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103145581","display_name":"T. N. Vijaykumar","orcid":"https://orcid.org/0000-0001-6624-4372"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. N. Vijaykumar","raw_affiliation_strings":["Purdue University"],"affiliations":[{"raw_affiliation_string":"Purdue University","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069139257","display_name":"Mithuna Thottethodi","orcid":"https://orcid.org/0000-0003-4164-4542"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mithuna Thottethodi","raw_affiliation_strings":["Purdue University"],"affiliations":[{"raw_affiliation_string":"Purdue University","institution_ids":["https://openalex.org/I219193219"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5060960403"],"corresponding_institution_ids":["https://openalex.org/I219193219"],"apc_list":null,"apc_paid":null,"fwci":0.4827,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.62298716,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9915000200271606,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9674000144004822,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/executor","display_name":"Executor","score":0.898659348487854},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8410780429840088},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7257279753684998},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5157480835914612},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5077005624771118},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.4589565396308899},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.4270242750644684},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4166269600391388},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.33819708228111267},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2431710660457611},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.18118777871131897}],"concepts":[{"id":"https://openalex.org/C180591056","wikidata":"https://www.wikidata.org/wiki/Q654437","display_name":"Executor","level":2,"score":0.898659348487854},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8410780429840088},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7257279753684998},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5157480835914612},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5077005624771118},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.4589565396308899},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.4270242750644684},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4166269600391388},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.33819708228111267},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2431710660457611},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.18118777871131897},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3458817.3476202","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3458817.3476202","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3458817.3476202","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3458817.3476202","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3458817.3476202","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3458817.3476202","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3209783322.pdf","grobid_xml":"https://content.openalex.org/works/W3209783322.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1978339264","https://openalex.org/W1983540755","https://openalex.org/W1994371611","https://openalex.org/W2019313821","https://openalex.org/W2024759417","https://openalex.org/W2037748100","https://openalex.org/W2039820867","https://openalex.org/W2043621752","https://openalex.org/W2055043387","https://openalex.org/W2068448872","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2110161565","https://openalex.org/W2111953042","https://openalex.org/W2166621589","https://openalex.org/W2260037449","https://openalex.org/W2270672919","https://openalex.org/W2344543892","https://openalex.org/W2408916298","https://openalex.org/W2515320923","https://openalex.org/W2613537099","https://openalex.org/W2784788330","https://openalex.org/W2789784730","https://openalex.org/W2791742850","https://openalex.org/W2900776157","https://openalex.org/W2938304012","https://openalex.org/W2981619930","https://openalex.org/W3033870872","https://openalex.org/W3043148535","https://openalex.org/W4214596219","https://openalex.org/W4229799243"],"related_works":["https://openalex.org/W2364921833","https://openalex.org/W2488897859","https://openalex.org/W2385146268","https://openalex.org/W1596201972","https://openalex.org/W1967954938","https://openalex.org/W2503642292","https://openalex.org/W2032980190","https://openalex.org/W1595151633","https://openalex.org/W2470589840","https://openalex.org/W2052334484"],"abstract_inverted_index":{"Recognizing":[0],"the":[1,8,76,89,97,144],"importance":[2],"of":[3,136],"whole":[4],"genome":[5],"alignment":[6,35,45],"(WGA),":[7],"National":[9],"Institutes":[10],"for":[11,28,122],"Health":[12],"maintains":[13],"LASTZ,":[14,146],"a":[15,25,56,69],"sequential":[16,145],"WGA":[17,59],"application.":[18],"As":[19],"genomic":[20],"data":[21],"grows,":[22],"there":[23],"is":[24,41,49],"compelling":[26],"need":[27],"scalable,":[29],"high-performance":[30],"WGA.":[31],"Unfortunately,":[32],"high-sensitivity,":[33],"`gapped'":[34],"which":[36,61,74],"uses":[37],"dynamic":[38],"programming":[39],"(DP)":[40],"slow,":[42],"whereas":[43],"faster":[44],"with":[46],"ungapped":[47],"filtering":[48],"often":[50],"less":[51],"sensitive.":[52],"We":[53],"develop":[54],"FastZ,":[55],"GPU-accelerated,":[57],"gapped":[58,63],"software":[60],"matches":[62],"LASTZ":[64,137],"in":[65,73,83],"sensitivity.":[66],"FastZ":[67,107,125],"employs":[68,108],"novel":[70],"inspector-executor":[71],"scheme":[72],"(a)":[75],"lightweight":[77],"inspector":[78,90],"elides":[79],"DP":[80,118],"traceback":[81,94],"except":[82],"common,":[84],"extremely":[85],"short":[86],"alignments,":[87],"where":[88],"performs":[91],"limited,":[92],"eager":[93],"to":[95,111],"eliminate":[96],"executor,":[98],"and":[99,116,132,140],"(b)":[100],"executor":[101],"trimming":[102],"avoids":[103],"unnecessary":[104],"work.":[105],"Further,":[106],"register-based":[109],"cyclic-buffering":[110],"drastically":[112],"reduce":[113],"memory":[114],"traffic,":[115],"groups":[117],"problems":[119],"by":[120],"size":[121],"load":[123],"balance.":[124],"running":[126],"on":[127],"an":[128],"RTX":[129],"3080":[130],"GPU":[131],"our":[133],"multicore":[134],"implementation":[135],"achieve":[138],"111x":[139],"20x":[141],"speedups":[142],"over":[143],"respectively.":[147]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2021-11-08T00:00:00"}