{"id":"https://openalex.org/W2775118504","doi":"https://doi.org/10.1109/bibm.2017.8217699","title":"GPU accelerated API for alignment of genomics sequencing data","display_name":"GPU accelerated API for alignment of genomics sequencing data","publication_year":2017,"publication_date":"2017-11-01","ids":{"openalex":"https://openalex.org/W2775118504","doi":"https://doi.org/10.1109/bibm.2017.8217699","mag":"2775118504"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2017.8217699","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8217699","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5101621413","display_name":"Nauman Ahmed","orcid":"https://orcid.org/0000-0002-3964-2348"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Nauman Ahmed","raw_affiliation_strings":["Computer Engineering Laboratory, Delft University of Technology, Delft, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Laboratory, Delft University of Technology, Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002503405","display_name":"Hamid Mushtaq","orcid":"https://orcid.org/0000-0003-4129-9056"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Hamid Mushtaq","raw_affiliation_strings":["Computer Engineering Laboratory, Delft University of Technology, Delft, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Laboratory, Delft University of Technology, Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058128591","display_name":"Koen Bertels","orcid":"https://orcid.org/0000-0001-9310-4885"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Koen Bertels","raw_affiliation_strings":["Computer Engineering Laboratory, Delft University of Technology, Delft, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Laboratory, Delft University of Technology, Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021955713","display_name":"Zaid Al-Ars","orcid":"https://orcid.org/0000-0001-7670-8572"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Zaid Al-Ars","raw_affiliation_strings":["Computer Engineering Laboratory, Delft University of Technology, Delft, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Laboratory, Delft University of Technology, Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I98358874"],"apc_list":null,"apc_paid":null,"fwci":3.6002,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.92873862,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"510","last_page":"515"},"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":0.9922999739646912,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9567999839782715,"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":0.8386508226394653},{"id":"https://openalex.org/keywords/simd","display_name":"SIMD","score":0.775596022605896},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.7179401516914368},{"id":"https://openalex.org/keywords/xeon-phi","display_name":"Xeon Phi","score":0.7091121673583984},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6961857080459595},{"id":"https://openalex.org/keywords/xeon","display_name":"Xeon","score":0.6790938973426819},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.607552170753479},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5371473431587219},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5222031474113464},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.49449774622917175},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.47114935517311096},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.4569329619407654},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.432841420173645},{"id":"https://openalex.org/keywords/instruction-set","display_name":"Instruction set","score":0.4284888803958893},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.4153318405151367},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.4120192527770996},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14119616150856018},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.14092710614204407},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.13983523845672607},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.0854756236076355}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8386508226394653},{"id":"https://openalex.org/C150552126","wikidata":"https://www.wikidata.org/wiki/Q339387","display_name":"SIMD","level":2,"score":0.775596022605896},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.7179401516914368},{"id":"https://openalex.org/C96972482","wikidata":"https://www.wikidata.org/wiki/Q1049168","display_name":"Xeon Phi","level":2,"score":0.7091121673583984},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6961857080459595},{"id":"https://openalex.org/C145108525","wikidata":"https://www.wikidata.org/wiki/Q656154","display_name":"Xeon","level":2,"score":0.6790938973426819},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.607552170753479},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5371473431587219},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5222031474113464},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.49449774622917175},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.47114935517311096},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.4569329619407654},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.432841420173645},{"id":"https://openalex.org/C202491316","wikidata":"https://www.wikidata.org/wiki/Q272683","display_name":"Instruction set","level":2,"score":0.4284888803958893},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.4153318405151367},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.4120192527770996},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14119616150856018},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.14092710614204407},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.13983523845672607},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0854756236076355},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2017.8217699","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8217699","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320316680","display_name":"University of Engineering and Technology, Lahore","ror":"https://ror.org/0051w2v06"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1573897044","https://openalex.org/W1596818353","https://openalex.org/W1599079562","https://openalex.org/W1850429294","https://openalex.org/W2040132285","https://openalex.org/W2044338118","https://openalex.org/W2065461987","https://openalex.org/W2146379626","https://openalex.org/W2160665949","https://openalex.org/W2170551349","https://openalex.org/W2260037449"],"related_works":["https://openalex.org/W2120385681","https://openalex.org/W2022113063","https://openalex.org/W2475524688","https://openalex.org/W2739740241","https://openalex.org/W2085105049","https://openalex.org/W2592417500","https://openalex.org/W1974923383","https://openalex.org/W2056079253","https://openalex.org/W2929736795","https://openalex.org/W1586106326"],"abstract_inverted_index":{"Sequence":[0],"alignment":[1,32,57],"is":[2,110,123],"a":[3,20,137],"core":[4],"step":[5],"in":[6,147],"the":[7,53,56,61,67,71,98,104,115],"processing":[8],"of":[9,26,33,55,66,92,101,140],"DNA":[10,34],"and":[11,35,59,63,79,131],"RNA":[12,36],"sequencing":[13,94],"data.":[14,95],"In":[15],"this":[16],"paper,":[17],"we":[18],"present":[19],"high":[21],"performance":[22],"GPU":[23],"accelerated":[24,42],"set":[25],"APIs":[27,40,144],"(GASAL)":[28],"for":[29,44,89],"pairwise":[30],"sequence":[31,90,105],"sequences.":[37],"The":[38,143],"GASAL":[39,69,96,122],"provide":[41],"kernels":[43],"local,":[45],"global":[46],"as":[47,49,77],"well":[48],"semi-global":[50],"alignment,":[51],"allowing":[52],"computation":[54],"score,":[58],"optionally":[60],"start":[62],"end":[64],"positions":[65],"alignment.":[68],"outperforms":[70,83],"fastest":[72],"CPU-optimized":[73],"SIMD":[74],"implementations":[75],"such":[76],"SSW":[78],"Parasail.":[80],"It":[81],"also":[82,102],"NVBIO,":[84],"NVIDIA's":[85],"own":[86],"CUDA":[87],"library":[88,152],"analysis":[91],"high-throughput":[93],"uses":[97],"unique":[99],"approach":[100],"performing":[103],"packing":[106],"on":[107,119],"GPU,":[108],"which":[109],"over":[111],"200\u00d7":[112],"faster":[113,125,133],"than":[114,126,134],"NVBIO":[116,135],"approach.":[117],"Overall":[118],"Tesla":[120],"K40c":[121],"10-14\u00d7":[124],"28":[127],"Intel":[128],"Xeon":[129],"cores":[130],"3-4\u00d7":[132],"with":[136],"query":[138],"length":[139],"100":[141],"bases.":[142],"are":[145],"included":[146],"an":[148],"easy":[149],"to":[150,153],"use":[151],"allow":[154],"integration":[155],"into":[156],"various":[157],"bioinformatics":[158],"tools.":[159]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
