{"id":"https://openalex.org/W2129713651","doi":"https://doi.org/10.1093/bioinformatics/btn032","title":"Compressed indexing and local alignment of DNA","display_name":"Compressed indexing and local alignment of DNA","publication_year":2008,"publication_date":"2008-01-28","ids":{"openalex":"https://openalex.org/W2129713651","doi":"https://doi.org/10.1093/bioinformatics/btn032","mag":"2129713651","pmid":"https://pubmed.ncbi.nlm.nih.gov/18227115"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn032","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn032","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/6/791/16886605/btn032.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/24/6/791/16886605/btn032.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077116003","display_name":"Tak\u2010Wah Lam","orcid":"https://orcid.org/0000-0003-4676-8587"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK","SG"],"is_corresponding":false,"raw_author_name":"T. W. Lam","raw_affiliation_strings":["1 Department of Computer Science, University of Hong Kong, Hong Kong, China and 2Department of Computer Science, National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Hong Kong, Hong Kong, China and 2Department of Computer Science, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012563463","display_name":"Wing\u2010Kin Sung","orcid":"https://orcid.org/0000-0001-7806-7086"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK","SG"],"is_corresponding":false,"raw_author_name":"W. K. Sung","raw_affiliation_strings":["1 Department of Computer Science, University of Hong Kong, Hong Kong, China and 2Department of Computer Science, National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Hong Kong, Hong Kong, China and 2Department of Computer Science, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069857248","display_name":"Siu-Lung Tam","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK","SG"],"is_corresponding":false,"raw_author_name":"S. L. Tam","raw_affiliation_strings":["1 Department of Computer Science, University of Hong Kong, Hong Kong, China and 2Department of Computer Science, National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Hong Kong, Hong Kong, China and 2Department of Computer Science, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111655137","display_name":"Ching Wong","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK","SG"],"is_corresponding":false,"raw_author_name":"C. K. Wong","raw_affiliation_strings":["1 Department of Computer Science, University of Hong Kong, Hong Kong, China and 2Department of Computer Science, National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Hong Kong, Hong Kong, China and 2Department of Computer Science, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596","https://openalex.org/I889458895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068137343","display_name":"SM Yiu","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK","SG"],"is_corresponding":false,"raw_author_name":"S. M. Yiu","raw_affiliation_strings":["1 Department of Computer Science, University of Hong Kong, Hong Kong, China and 2Department of Computer Science, National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Hong Kong, Hong Kong, China and 2Department of Computer Science, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596","https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":18.2204,"has_fulltext":true,"cited_by_count":133,"citation_normalized_percentile":{"value":0.99212704,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"24","issue":"6","first_page":"791","last_page":"797"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9757000207901001,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9757000207901001,"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/T12205","display_name":"Time Series Analysis and Forecasting","score":0.002899999963119626,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.0027000000700354576,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/substring","display_name":"Substring","score":0.858683705329895},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.7644531726837158},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6892580389976501},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5777910947799683},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.5574281811714172},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.5428355932235718},{"id":"https://openalex.org/keywords/byte","display_name":"Byte","score":0.5058597922325134},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.47997379302978516},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.47680068016052246},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4645395576953888},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.4530593156814575},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.44283390045166016},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.42065536975860596},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.413442462682724},{"id":"https://openalex.org/keywords/string-searching-algorithm","display_name":"String searching algorithm","score":0.41292911767959595},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33203646540641785},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.3144441246986389},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2832796573638916},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.25080615282058716},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20300734043121338},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1932927668094635},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14508011937141418},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12383866310119629},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.11193004250526428}],"concepts":[{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.858683705329895},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.7644531726837158},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6892580389976501},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5777910947799683},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.5574281811714172},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.5428355932235718},{"id":"https://openalex.org/C43364308","wikidata":"https://www.wikidata.org/wiki/Q8799","display_name":"Byte","level":2,"score":0.5058597922325134},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.47997379302978516},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.47680068016052246},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4645395576953888},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.4530593156814575},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.44283390045166016},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.42065536975860596},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.413442462682724},{"id":"https://openalex.org/C7757238","wikidata":"https://www.wikidata.org/wiki/Q374040","display_name":"String searching algorithm","level":3,"score":0.41292911767959595},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33203646540641785},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.3144441246986389},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2832796573638916},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.25080615282058716},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20300734043121338},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1932927668094635},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14508011937141418},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12383866310119629},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.11193004250526428},{"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/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btn032","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn032","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/6/791/16886605/btn032.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:18227115","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18227115","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},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/39850","is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/39850","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus","raw_type":"Article"},{"id":"pmh:oai:hub.hku.hk:10722/89140","is_oa":false,"landing_page_url":"http://hdl.handle.net/10722/89140","pdf_url":null,"source":{"id":"https://openalex.org/S4377196271","display_name":"The HKU Scholars Hub (University of Hong Kong)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I889458895","host_organization_name":"University of Hong Kong","host_organization_lineage":["https://openalex.org/I889458895"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn032","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn032","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/6/791/16886605/btn032.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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2129713651.pdf","grobid_xml":"https://content.openalex.org/works/W2129713651.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1490635997","https://openalex.org/W1557034006","https://openalex.org/W1603784832","https://openalex.org/W1909344111","https://openalex.org/W1955121107","https://openalex.org/W2013697960","https://openalex.org/W2017808314","https://openalex.org/W2028445324","https://openalex.org/W2030428223","https://openalex.org/W2030962049","https://openalex.org/W2046038806","https://openalex.org/W2055043387","https://openalex.org/W2056707490","https://openalex.org/W2068421750","https://openalex.org/W2081484203","https://openalex.org/W2087064593","https://openalex.org/W2091273836","https://openalex.org/W2094519647","https://openalex.org/W2108235229","https://openalex.org/W2121252285","https://openalex.org/W2127465481","https://openalex.org/W2131989567","https://openalex.org/W2142313803","https://openalex.org/W2143642163","https://openalex.org/W2158322625","https://openalex.org/W2158714788","https://openalex.org/W2161488606","https://openalex.org/W2170899819","https://openalex.org/W2610179052","https://openalex.org/W6629219293","https://openalex.org/W6639872743","https://openalex.org/W6654031322","https://openalex.org/W6674269648","https://openalex.org/W6681018127","https://openalex.org/W6683030939"],"related_works":["https://openalex.org/W164375046","https://openalex.org/W52396946","https://openalex.org/W2298204719","https://openalex.org/W2902482624","https://openalex.org/W2902555313","https://openalex.org/W2376315482","https://openalex.org/W4249054680","https://openalex.org/W3112977702","https://openalex.org/W2218650848","https://openalex.org/W2366227422"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recent":[1],"experimental":[2],"studies":[3],"on":[4,68],"compressed":[5],"indexes":[6,50],"(BWT,":[7],"CSA,":[8],"FM-index)":[9],"have":[10,211,287],"confirmed":[11],"their":[12],"practicality":[13],"for":[14,33,53,61,181,216,234,274],"indexing":[15],"very":[16,142,191],"long":[17,275],"strings":[18],"such":[19,137],"as":[20,138,239,265],"the":[21,25,34,89,110,121,178,202,228,244,293],"human":[22,35,122,203],"genome":[23,36,114,123,204],"in":[24,100,283],"main":[26],"memory.":[27],"For":[28],"example,":[29],"a":[30,93,97,118,162,168,172,195,208,217,261],"BWT":[31,169],"index":[32,170],"(with":[37,221],"about":[38],"3":[39,199],"billion":[40],"characters)":[41],"occupies":[42],"just":[43],"around":[44],"1":[45],"G":[46],"bytes.":[47],"However,":[48],"these":[49],"are":[51],"designed":[52],"exact":[54],"pattern":[55,98,196],"matching,":[56],"which":[57,140],"is":[58,66,112,141,190,232,243,256,267,279],"too":[59,107],"stringent":[60],"biological":[62],"applications.":[63],"The":[64],"demand":[65],"often":[67],"finding":[69,182],"local":[70,90,151,184,252],"alignments":[71,91],"(pairs":[72],"of":[73,113,129,171,197,263,295],"similar":[74],"substrings":[75],"with":[76,120,201],"gaps":[77,222],"allowed).":[78],"Without":[79],"indexing,":[80],"one":[81],"can":[82,249],"use":[83,134],"dynamic":[84,179],"programming":[85,180],"to":[86,127,148,160,175,259,290],"find":[87,149,250],"all":[88,150,183,251],"between":[92],"text":[94,111,173],"T":[95,174],"and":[96,224,277,297],"P":[99],"O(|T||P|)":[101],"time,":[102],"but":[103,144],"this":[104,155],"would":[105,124,303],"be":[106,260],"slow":[108],"when":[109],"scale":[115],"(e.g.":[116,193],"aligning":[117,194],"gene":[119],"take":[125],"tens":[126],"hundreds":[128],"hours).":[130],"In":[131,154],"practice,":[132],"biologists":[133],"heuristic-based":[135],"software":[136,163],"BLAST,":[139,264],"efficient":[143,192],"does":[145],"not":[146,257],"guarantee":[147],"alignments.":[152,185,253],"RESULTS:":[153],"article,":[156],"we":[157,225,240],"show":[158,226],"how":[159],"build":[161],"called":[164],"BWT-SW":[165,189,214,242,255,273,289],"that":[166,188,227,248,299],"exploits":[167],"speed":[176],"up":[177],"Experiments":[186],"reveal":[187],"length":[198],"000":[200],"takes":[205],"less":[206],"than":[207,272],"minute).":[209],"We":[210],"also":[212],"analyzed":[213],"mathematically":[215],"simpler":[218],"similarity":[219],"model":[220],"disallowed),":[223],"expected":[229],"running":[230],"time":[231],"O(/T/(0.628)/P/)":[233],"random":[235],"strings.":[236],"As":[237],"far":[238],"know,":[241],"first":[245],"practical":[246],"tool":[247],"Yet":[254],"meant":[258],"replacement":[262],"BLAST":[266,278,296,302],"still":[268],"several":[269],"times":[270],"faster":[271],"patterns":[276],"indeed":[280],"accurate":[281],"enough":[282],"most":[284],"cases":[285],"(we":[286],"used":[288],"check":[291],"against":[292],"accuracy":[294],"found":[298],"only":[300],"rarely":[301],"miss":[304],"some":[305],"significant":[306],"alignments).":[307],"AVAILABILITY:":[308],"www.cs.hku.hk/~ckwong3/bwtsw":[309],"CONTACT:":[310],"twlam@cs.hku.hk.":[311]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":13},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":24}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
