{"id":"https://openalex.org/W2119247498","doi":"https://doi.org/10.1093/bioinformatics/bth308","title":"An efficient algorithm for optimizing whole genome alignment with noise","display_name":"An efficient algorithm for optimizing whole genome alignment with noise","publication_year":2004,"publication_date":"2004-05-14","ids":{"openalex":"https://openalex.org/W2119247498","doi":"https://doi.org/10.1093/bioinformatics/bth308","mag":"2119247498","pmid":"https://pubmed.ncbi.nlm.nih.gov/15145812"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth308","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth308","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063692696","display_name":"Prudence W. H. Wong","orcid":"https://orcid.org/0000-0001-7935-7245"},"institutions":[{"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"],"is_corresponding":true,"raw_author_name":"Prudence W. H. Wong","raw_affiliation_strings":["Department of Computer Science, University of Hong Kong, Hong Kong","Department of Computer Science, University of Hong Kong, Hong Kong,#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Computer Science, University of Hong Kong, Hong Kong,#TAB#","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077116003","display_name":"Tak\u2010Wah Lam","orcid":"https://orcid.org/0000-0003-4676-8587"},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"T. W. Lam","raw_affiliation_strings":["Department of Computer Science, University of Hong Kong, Hong Kong","Department of Computer Science, University of Hong Kong, Hong Kong,#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Computer Science, University of Hong Kong, Hong Kong,#TAB#","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100432414","display_name":"Ning L\u00fc","orcid":"https://orcid.org/0000-0003-0125-0653"},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"N. Lu","raw_affiliation_strings":["Department of Computer Science, University of Hong Kong, Hong Kong","Department of Computer Science, University of Hong Kong, Hong Kong,#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Computer Science, University of Hong Kong, Hong Kong,#TAB#","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033934413","display_name":"Hing\u2010Fung Ting","orcid":"https://orcid.org/0000-0002-2807-2351"},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"H. F. Ting","raw_affiliation_strings":["Department of Computer Science, University of Hong Kong, Hong Kong","Department of Computer Science, University of Hong Kong, Hong Kong,#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Computer Science, University of Hong Kong, Hong Kong,#TAB#","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110500992","display_name":"Siu\u2010Ming Yiu","orcid":null},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"S. M. Yiu","raw_affiliation_strings":["Department of Computer Science, University of Hong Kong, Hong Kong","Department of Computer Science, University of Hong Kong, Hong Kong,#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Computer Science, University of Hong Kong, Hong Kong,#TAB#","institution_ids":["https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5063692696"],"corresponding_institution_ids":["https://openalex.org/I889458895"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6029,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.65772101,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"20","issue":"16","first_page":"2676","last_page":"2684"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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":0.9986000061035156,"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":0.9958999752998352,"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":0.9958000183105469,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6745956540107727},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.6483693718910217},{"id":"https://openalex.org/keywords/genbank","display_name":"GenBank","score":0.6331706047058105},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.625603437423706},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5926561951637268},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5386455059051514},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.46920862793922424},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4570190906524658},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.44604766368865967},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4437037706375122},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.363631010055542},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2444760799407959},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2102189064025879},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1914764642715454},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.1751055121421814},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16943135857582092},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10115402936935425}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6745956540107727},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.6483693718910217},{"id":"https://openalex.org/C79029880","wikidata":"https://www.wikidata.org/wiki/Q901755","display_name":"GenBank","level":3,"score":0.6331706047058105},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.625603437423706},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5926561951637268},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5386455059051514},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.46920862793922424},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4570190906524658},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.44604766368865967},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4437037706375122},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.363631010055542},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2444760799407959},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2102189064025879},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1914764642715454},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.1751055121421814},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16943135857582092},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10115402936935425},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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":"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":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"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":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/bth308","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth308","pdf_url":null,"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:15145812","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15145812","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:CiteSeerX.psu:10.1.1.131.8658","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.131.8658","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.hku.hk/~mss/paper/wga.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.617.6014","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.617.6014","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/20/16/2676.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.977.6394","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.977.6394","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://hub.hku.hk/bitstream/10722/43629/1/107321.pdf","raw_type":"text"},{"id":"pmh:oai:hub.hku.hk:10722/43629","is_oa":false,"landing_page_url":"http://hdl.handle.net/10722/43629","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":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4399999976158142}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1632341477","https://openalex.org/W1652529314","https://openalex.org/W1964918240","https://openalex.org/W1974490028","https://openalex.org/W1986014242","https://openalex.org/W1990061958","https://openalex.org/W1998365429","https://openalex.org/W2025729362","https://openalex.org/W2035169994","https://openalex.org/W2036295979","https://openalex.org/W2063822318","https://openalex.org/W2074231493","https://openalex.org/W2095685450","https://openalex.org/W2100680075","https://openalex.org/W2107282968","https://openalex.org/W2109034006","https://openalex.org/W2116688916","https://openalex.org/W2152331922","https://openalex.org/W2158714788","https://openalex.org/W2517000487"],"related_works":["https://openalex.org/W3033962221","https://openalex.org/W2737894786","https://openalex.org/W2796038416","https://openalex.org/W3095372394","https://openalex.org/W2366828174","https://openalex.org/W653670262","https://openalex.org/W3006459298","https://openalex.org/W2124899825","https://openalex.org/W959908619","https://openalex.org/W977967403"],"abstract_inverted_index":{"The":[0],"source":[1],"code":[2],"is":[3],"available":[4],"from":[5],"the":[6,12],"website":[7],"http://www.csis.hku.hk/~colly/maxmincluster/":[8],"detailed":[9],"proof":[10],"of":[11],"propositions":[13],"can":[14],"also":[15],"be":[16],"found":[17],"there.":[18]},"counts_by_year":[],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}