{"id":"https://openalex.org/W2979985440","doi":"https://doi.org/10.1145/3360551","title":"Seq: a high-performance language for bioinformatics","display_name":"Seq: a high-performance language for bioinformatics","publication_year":2019,"publication_date":"2019-10-10","ids":{"openalex":"https://openalex.org/W2979985440","doi":"https://doi.org/10.1145/3360551","mag":"2979985440","pmid":"https://pubmed.ncbi.nlm.nih.gov/35775031"},"language":"en","primary_location":{"id":"doi:10.1145/3360551","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3360551","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3360551","source":{"id":"https://openalex.org/S4210216081","display_name":"Proceedings of the ACM on Programming Languages","issn_l":"2475-1421","issn":["2475-1421"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"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 ACM on Programming Languages","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3360551","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061029430","display_name":"Ariya Shajii","orcid":"https://orcid.org/0000-0002-6163-1848"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ariya Shajii","raw_affiliation_strings":["Massachusetts Institute of Technology, USA"],"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060847860","display_name":"Ibrahim Numanagi\u0107","orcid":"https://orcid.org/0000-0002-2970-7937"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ibrahim Numanagi\u0107","raw_affiliation_strings":["Massachusetts Institute of Technology, USA"],"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044704994","display_name":"Riyadh Baghdadi","orcid":"https://orcid.org/0000-0002-9350-3998"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Riyadh Baghdadi","raw_affiliation_strings":["Massachusetts Institute of Technology, USA"],"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044078921","display_name":"Bonnie Berger","orcid":"https://orcid.org/0000-0002-2724-7228"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bonnie Berger","raw_affiliation_strings":["Massachusetts Institute of Technology, USA"],"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046791216","display_name":"Saman Amarasinghe","orcid":"https://orcid.org/0000-0002-7231-7643"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Saman Amarasinghe","raw_affiliation_strings":["Massachusetts Institute of Technology, USA"],"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology, USA","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5061029430"],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":null,"apc_paid":null,"fwci":0.8589,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.73297936,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"3","issue":"OOPSLA","first_page":"1","last_page":"29"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9983999729156494,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9927999973297119,"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":0.5851555466651917},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.4117279350757599},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35944122076034546},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3424246609210968},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23733848333358765}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5851555466651917},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4117279350757599},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35944122076034546},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3424246609210968},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23733848333358765}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1145/3360551","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3360551","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3360551","source":{"id":"https://openalex.org/S4210216081","display_name":"Proceedings of the ACM on Programming Languages","issn_l":"2475-1421","issn":["2475-1421"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"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 ACM on Programming Languages","raw_type":"journal-article"},{"id":"pmid:35775031","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35775031","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the ACM on programming languages","raw_type":null},{"id":"pmh:oai:dspace.mit.edu:1721.1/132251","is_oa":true,"landing_page_url":"https://hdl.handle.net/1721.1/132251","pdf_url":null,"source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM","raw_type":"Article"},{"id":"pmh:oai:dspace.mit.edu:1721.1/132251.2","is_oa":true,"landing_page_url":"https://hdl.handle.net/1721.1/132251.2","pdf_url":null,"source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9241673","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9241673","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc ACM Program Lang","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1145/3360551","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3360551","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3360551","source":{"id":"https://openalex.org/S4210216081","display_name":"Proceedings of the ACM on Programming Languages","issn_l":"2475-1421","issn":["2475-1421"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"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 ACM on Programming Languages","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320312414","display_name":"Oxford Nanopore Technologies","ror":"https://ror.org/04hyfx005"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2979985440.pdf","grobid_xml":"https://content.openalex.org/works/W2979985440.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W53860051","https://openalex.org/W193231727","https://openalex.org/W1489951562","https://openalex.org/W1976369775","https://openalex.org/W1978251004","https://openalex.org/W1993335798","https://openalex.org/W2005907808","https://openalex.org/W2008985174","https://openalex.org/W2009501359","https://openalex.org/W2055312318","https://openalex.org/W2075996757","https://openalex.org/W2093931624","https://openalex.org/W2099580433","https://openalex.org/W2101983393","https://openalex.org/W2103441770","https://openalex.org/W2104266030","https://openalex.org/W2108234281","https://openalex.org/W2114850508","https://openalex.org/W2115501618","https://openalex.org/W2116412478","https://openalex.org/W2119180969","https://openalex.org/W2121984048","https://openalex.org/W2123516016","https://openalex.org/W2143788241","https://openalex.org/W2146379626","https://openalex.org/W2151318268","https://openalex.org/W2153185479","https://openalex.org/W2162569557","https://openalex.org/W2165693128","https://openalex.org/W2171777347","https://openalex.org/W2245493112","https://openalex.org/W2264578395","https://openalex.org/W2302703011","https://openalex.org/W2320964193","https://openalex.org/W2406493898","https://openalex.org/W2412192467","https://openalex.org/W2521004200","https://openalex.org/W2569156823","https://openalex.org/W2581356531","https://openalex.org/W2585769337","https://openalex.org/W2593170933","https://openalex.org/W2751416425","https://openalex.org/W2767274246","https://openalex.org/W2788876413","https://openalex.org/W2791742850","https://openalex.org/W2885727518","https://openalex.org/W2888362217","https://openalex.org/W2897764559","https://openalex.org/W2898231337","https://openalex.org/W2949967139","https://openalex.org/W2950150251","https://openalex.org/W2950294163","https://openalex.org/W2953174564","https://openalex.org/W2972874842","https://openalex.org/W4237194902","https://openalex.org/W4238737563","https://openalex.org/W4244568863","https://openalex.org/W4246166885","https://openalex.org/W4251637954","https://openalex.org/W4254172385"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"The":[0],"scope":[1],"and":[2,22,110,128,153,160,179,189,215,236,244,279],"scale":[3],"of":[4,32,45,50,80,130,140,185,229,234,292,294],"biological":[5,81,93],"data":[6,51,156],"are":[7,18,89,246],"increasing":[8],"at":[9],"an":[10,290],"exponential":[11],"rate,":[12],"as":[13,59],"technologies":[14],"like":[15,207],"next-generation":[16],"sequencing":[17,33],"becoming":[19],"radically":[20],"cheaper":[21],"more":[23],"prevalent.":[24],"Over":[25],"the":[26,30,48,77,98,117,126,182,186,287],"last":[27],"two":[28,232],"decades,":[29],"cost":[31],"a":[34,84,138,146,226,237,254,276],"genome":[35],"has":[36,55],"dropped":[37],"from":[38],"$100":[39],"million":[40],"to":[41,52,63,74,101,106,122,165,172,231,253,258,269,275,289],"nearly":[42],"$100-a":[43],"factor":[44],"over":[46,95],"10<sup>6</sup>-and":[47],"amount":[49],"be":[53],"analyzed":[54],"increased":[56],"proportionally.":[57],"Yet,":[58],"Moore's":[60],"Law":[61],"continues":[62],"slow,":[64],"computational":[65,96,154,204],"biologists":[66,268],"can":[67],"no":[68],"longer":[69],"rely":[70],"on":[71,92,201],"computing":[72],"hardware":[73],"compensate":[75],"for":[76,181,266],"ever-increasing":[78],"size":[79],"datasets.":[82],"In":[83],"field":[85],"where":[86],"many":[87,144,193],"researchers":[88],"primarily":[90],"focused":[91],"analysis":[94],"optimization,":[97],"unfortunate":[99],"solution":[100],"this":[102],"problem":[103],"is":[104,142,263],"often":[105],"simply":[107],"buy":[108],"larger":[109],"faster":[111],"machines.":[112],"Here,":[113],"we":[114,250],"introduce":[115],"Seq,":[116],"first":[118],"language":[119,158,242],"tailored":[120],"specifically":[121],"bioinformatics,":[123],"which":[124,262],"marries":[125],"ease":[127],"productivity":[129],"Python":[131],"with":[132,137,280],"C-like":[133],"performance.":[134],"Seq":[135,162,200,224,271,285],"starts":[136],"subset":[139],"Python-and":[141],"in":[143,192],"cases":[145],"drop-in":[147],"replacement-yet":[148],"also":[149],"incorporates":[150],"novel":[151],"bioinformatics-":[152],"genomics-oriented":[155],"types,":[157],"constructs":[159],"optimizations.":[161],"enables":[163],"users":[164],"write":[166],"high-level,":[167],"Pythonic":[168],"code":[169],"without":[170],"having":[171],"worry":[173],"about":[174],"low-level":[175],"or":[176,195],"domain-specific":[177,241],"optimizations,":[178],"allows":[180],"seamless":[183],"expression":[184],"algorithms,":[187],"idioms":[188],"patterns":[190],"found":[191],"genomics":[194,205],"bioinformatics":[196,296],"applications.":[197],"We":[198],"evaluated":[199],"several":[202],"standard":[203],"tasks":[206],"reverse":[208],"complementation,":[209],"<i>k</i>-mer":[210],"manipulation,":[211],"sequence":[212],"pattern":[213],"matching":[214],"large":[216],"genomic":[217],"index":[218],"queries.":[219],"On":[220],"equivalent":[221],"CPython":[222],"code,":[223,261],"attains":[225,273],"performance":[227],"improvement":[228,239],"up":[230,252,274],"orders":[233],"magnitude,":[235],"160\u00d7":[238],"once":[240],"features":[243],"optimizations":[245],"used.":[247],"With":[248],"parallelism,":[249],"demonstrate":[251],"650\u00d7":[255],"improvement.":[256],"Compared":[257],"optimized":[259],"C++":[260],"already":[264],"difficult":[265],"most":[267],"produce,":[270],"frequently":[272],"2\u00d7":[277],"improvement,":[278],"shorter,":[281],"cleaner":[282],"code.":[283],"Thus,":[284],"opens":[286],"door":[288],"age":[291],"democratization":[293],"highly-optimized":[295],"software.":[297]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
