{"id":"https://openalex.org/W3106484143","doi":"https://doi.org/10.1093/bioinformatics/btaa963","title":"abPOA: an SIMD-based C library for fast partial order alignment using adaptive band","display_name":"abPOA: an SIMD-based C library for fast partial order alignment using adaptive band","publication_year":2020,"publication_date":"2020-11-03","ids":{"openalex":"https://openalex.org/W3106484143","doi":"https://doi.org/10.1093/bioinformatics/btaa963","mag":"3106484143","pmid":"https://pubmed.ncbi.nlm.nih.gov/33165528"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa963","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa963","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/15/2209/40080650/btaa963.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/15/2209/40080650/btaa963.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062662220","display_name":"Yan Gao","orcid":"https://orcid.org/0000-0003-3814-5750"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]},{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I4210161462","display_name":"Heilongjiang Institute of Technology","ror":"https://ror.org/05x0m9n95","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210161462"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yan Gao","raw_affiliation_strings":["Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology , Harbin, Heilongjiang 150001, China","Center for Computational and Genomic Medicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, USA"],"raw_orcid":"https://orcid.org/0000-0003-3814-5750","affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology , Harbin, Heilongjiang 150001, China","institution_ids":["https://openalex.org/I4210161462","https://openalex.org/I204983213"]},{"raw_affiliation_string":"Center for Computational and Genomic Medicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009730904","display_name":"Yongzhuang Liu","orcid":"https://orcid.org/0000-0002-2572-7420"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I4210161462","display_name":"Heilongjiang Institute of Technology","ror":"https://ror.org/05x0m9n95","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210161462"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongzhuang Liu","raw_affiliation_strings":["Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology , Harbin, Heilongjiang 150001, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology , Harbin, Heilongjiang 150001, China","institution_ids":["https://openalex.org/I4210161462","https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101029133","display_name":"Yanmei Ma","orcid":"https://orcid.org/0009-0007-6948-8576"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I4210161462","display_name":"Heilongjiang Institute of Technology","ror":"https://ror.org/05x0m9n95","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210161462"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanmei Ma","raw_affiliation_strings":["Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology , Harbin, Heilongjiang 150001, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology , Harbin, Heilongjiang 150001, China","institution_ids":["https://openalex.org/I4210161462","https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100461657","display_name":"Bo Liu","orcid":"https://orcid.org/0000-0002-4414-4001"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I4210161462","display_name":"Heilongjiang Institute of Technology","ror":"https://ror.org/05x0m9n95","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210161462"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Liu","raw_affiliation_strings":["Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology , Harbin, Heilongjiang 150001, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology , Harbin, Heilongjiang 150001, China","institution_ids":["https://openalex.org/I4210161462","https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392447","display_name":"Yadong Wang","orcid":"https://orcid.org/0000-0001-6500-6217"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I4210161462","display_name":"Heilongjiang Institute of Technology","ror":"https://ror.org/05x0m9n95","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210161462"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yadong Wang","raw_affiliation_strings":["Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology , Harbin, Heilongjiang 150001, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Department of Computer Science and Technology, Harbin Institute of Technology , Harbin, Heilongjiang 150001, China","institution_ids":["https://openalex.org/I4210161462","https://openalex.org/I204983213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087568641","display_name":"Yi Xing","orcid":"https://orcid.org/0000-0001-9257-7613"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yi Xing","raw_affiliation_strings":["Center for Computational and Genomic Medicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, USA","Department of Pathology and Laboratory Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational and Genomic Medicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5087568641","https://openalex.org/A5100392447"],"corresponding_institution_ids":["https://openalex.org/I1335321130","https://openalex.org/I204983213","https://openalex.org/I4210161462","https://openalex.org/I79576946"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.7087,"has_fulltext":false,"cited_by_count":56,"citation_normalized_percentile":{"value":0.849575,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"37","issue":"15","first_page":"2209","last_page":"2211"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6535000205039978,"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":0.6535000205039978,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.06949999928474426,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.051600001752376556,"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/simd","display_name":"SIMD","score":0.8726691007614136},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7772204279899597},{"id":"https://openalex.org/keywords/order","display_name":"Order (exchange)","score":0.658355712890625},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.443771094083786},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.35888367891311646},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.33263063430786133},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20642966032028198}],"concepts":[{"id":"https://openalex.org/C150552126","wikidata":"https://www.wikidata.org/wiki/Q339387","display_name":"SIMD","level":2,"score":0.8726691007614136},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7772204279899597},{"id":"https://openalex.org/C182306322","wikidata":"https://www.wikidata.org/wiki/Q1779371","display_name":"Order (exchange)","level":2,"score":0.658355712890625},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.443771094083786},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.35888367891311646},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.33263063430786133},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20642966032028198},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa963","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa963","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/15/2209/40080650/btaa963.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33165528","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33165528","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa963","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa963","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/15/2209/40080650/btaa963.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2524202503","display_name":null,"funder_award_id":"2017YFC0907503","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G3616348304","display_name":null,"funder_award_id":"2017YFC1201201","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G4440211012","display_name":null,"funder_award_id":"2018YFC0910504","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5147852514","display_name":null,"funder_award_id":"31701147","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320309099","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2141978199","https://openalex.org/W2142113273","https://openalex.org/W2146696273","https://openalex.org/W2153242254","https://openalex.org/W2575750030","https://openalex.org/W2611922188","https://openalex.org/W2891014523","https://openalex.org/W2950266744","https://openalex.org/W2955242233","https://openalex.org/W3017512083","https://openalex.org/W3088400220"],"related_works":["https://openalex.org/W2291920536","https://openalex.org/W2022397046","https://openalex.org/W2162726111","https://openalex.org/W1603583590","https://openalex.org/W338671845","https://openalex.org/W1587248296","https://openalex.org/W2117755361","https://openalex.org/W2286348849","https://openalex.org/W2063770303","https://openalex.org/W2018511057"],"abstract_inverted_index":{"SUMMARY:":[0],"Partial":[1,32],"order":[2,46],"alignment,":[3],"which":[4],"aligns":[5],"a":[6,9,18,35,57,80,92,108],"sequence":[7,60],"to":[8,79,87],"directed":[10],"acyclic":[11],"graph,":[12],"is":[13,85,100],"now":[14],"frequently":[15],"used":[16],"as":[17,56],"key":[19],"component":[20],"in":[21,102],"long-read":[22,72],"error":[23,73],"correction":[24,74],"and":[25,62,75,107],"assembly.":[26],"We":[27],"present":[28],"abPOA":[29,84,99],"(adaptive":[30],"banded":[31,50],"Order":[33],"Alignment),":[34],"Single":[36],"Instruction":[37],"Multiple":[38],"Data":[39],"(SIMD)-based":[40],"C":[41],"library":[42],"for":[43],"fast":[44],"partial":[45],"alignment":[47,61,94],"using":[48],"adaptive":[49],"dynamic":[51],"programming.":[52],"It":[53],"can":[54],"work":[55],"stand-alone":[58,105],"multiple":[59],"consensus":[63],"calling":[64],"tool":[65,82,106],"or":[66],"be":[67],"easily":[68],"integrated":[69],"into":[70],"any":[71],"assembly":[76],"workflow.":[77],"Compared":[78],"state-of-the-art":[81],"(SPOA),":[83],"up":[86],"10":[88],"times":[89],"faster":[90],"with":[91],"comparable":[93],"accuracy.":[95],"AVAILABILITY":[96],"AND":[97],"IMPLEMENTATION:":[98],"implemented":[101],"C.":[103],"A":[104],"C/Python":[109],"software":[110],"interface":[111],"are":[112,121],"freely":[113],"available":[114,122],"at":[115,123],"https://github.com/yangao07/abPOA.":[116],"SUPPLEMENTARY":[117],"INFORMATION:":[118],"Supplementary":[119],"data":[120],"Bioinformatics":[124],"online.":[125]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":3}],"updated_date":"2026-07-14T08:27:34.040176","created_date":"2025-10-10T00:00:00"}
