{"id":"https://openalex.org/W2121305702","doi":"https://doi.org/10.1093/bioinformatics/btp054","title":"Fast computation of neighbor seeds","display_name":"Fast computation of neighbor seeds","publication_year":2009,"publication_date":"2009-01-28","ids":{"openalex":"https://openalex.org/W2121305702","doi":"https://doi.org/10.1093/bioinformatics/btp054","mag":"2121305702","pmid":"https://pubmed.ncbi.nlm.nih.gov/19176560"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp054","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp054","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/6/822/50286701/bioinformatics_25_6_822.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/25/6/822/50286701/bioinformatics_25_6_822.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048178906","display_name":"Lucian Ilie","orcid":"https://orcid.org/0000-0003-1856-3509"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I530967","display_name":"Toronto Metropolitan University","ror":"https://ror.org/05g13zd79","country_code":"CA","type":"education","lineage":["https://openalex.org/I530967"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Lucian Ilie","raw_affiliation_strings":["1 Department of Computer Science, University of Western Ontario, London N6A 5B7 and 2Department of Mathematics, Ryerson University, Toronto, M5B 2K3, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Western Ontario, London N6A 5B7 and 2Department of Mathematics, Ryerson University, Toronto, M5B 2K3, Ontario, Canada","institution_ids":["https://openalex.org/I530967","https://openalex.org/I125749732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087482165","display_name":"Silvana Ilie","orcid":"https://orcid.org/0009-0002-1220-5479"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I530967","display_name":"Toronto Metropolitan University","ror":"https://ror.org/05g13zd79","country_code":"CA","type":"education","lineage":["https://openalex.org/I530967"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Silvana Ilie","raw_affiliation_strings":["1 Department of Computer Science, University of Western Ontario, London N6A 5B7 and 2Department of Mathematics, Ryerson University, Toronto, M5B 2K3, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, University of Western Ontario, London N6A 5B7 and 2Department of Mathematics, Ryerson University, Toronto, M5B 2K3, Ontario, Canada","institution_ids":["https://openalex.org/I530967","https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5048178906"],"corresponding_institution_ids":["https://openalex.org/I125749732","https://openalex.org/I530967"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1369,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.55983011,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"25","issue":"6","first_page":"822","last_page":"823"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"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":0.9980000257492065,"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":0.9976999759674072,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9702000021934509,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.7239354252815247},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.6763212084770203},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.666154146194458},{"id":"https://openalex.org/keywords/exponential-function","display_name":"Exponential function","score":0.609710693359375},{"id":"https://openalex.org/keywords/current","display_name":"Current (fluid)","score":0.5805519819259644},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.5711028575897217},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5201594829559326},{"id":"https://openalex.org/keywords/exponential-growth","display_name":"Exponential growth","score":0.4981858730316162},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.483452171087265},{"id":"https://openalex.org/keywords/k-nearest-neighbors-algorithm","display_name":"k-nearest neighbors algorithm","score":0.47593215107917786},{"id":"https://openalex.org/keywords/polynomial","display_name":"Polynomial","score":0.47197017073631287},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.45244118571281433},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3021396994590759},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.242925763130188}],"concepts":[{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.7239354252815247},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.6763212084770203},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.666154146194458},{"id":"https://openalex.org/C151376022","wikidata":"https://www.wikidata.org/wiki/Q168698","display_name":"Exponential function","level":2,"score":0.609710693359375},{"id":"https://openalex.org/C148043351","wikidata":"https://www.wikidata.org/wiki/Q4456944","display_name":"Current (fluid)","level":2,"score":0.5805519819259644},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.5711028575897217},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5201594829559326},{"id":"https://openalex.org/C75235859","wikidata":"https://www.wikidata.org/wiki/Q582659","display_name":"Exponential growth","level":2,"score":0.4981858730316162},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.483452171087265},{"id":"https://openalex.org/C113238511","wikidata":"https://www.wikidata.org/wiki/Q1071612","display_name":"k-nearest neighbors algorithm","level":2,"score":0.47593215107917786},{"id":"https://openalex.org/C90119067","wikidata":"https://www.wikidata.org/wiki/Q43260","display_name":"Polynomial","level":2,"score":0.47197017073631287},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.45244118571281433},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3021396994590759},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.242925763130188},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp054","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp054","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/6/822/50286701/bioinformatics_25_6_822.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:19176560","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19176560","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:10.1.1.149.5356","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.149.5356","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.csd.uwo.ca/faculty/ilie/BIOINF09.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp054","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp054","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/6/822/50286701/bioinformatics_25_6_822.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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2121305702.pdf","grobid_xml":"https://content.openalex.org/works/W2121305702.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1955121107","https://openalex.org/W2029195137","https://openalex.org/W2055043387","https://openalex.org/W2068235693","https://openalex.org/W2074231493","https://openalex.org/W2076795608","https://openalex.org/W2087064593","https://openalex.org/W2106532429","https://openalex.org/W2128591967","https://openalex.org/W2131989567"],"related_works":["https://openalex.org/W1634993130","https://openalex.org/W1602624896","https://openalex.org/W32300376","https://openalex.org/W1519862060","https://openalex.org/W1974979356","https://openalex.org/W2084061773","https://openalex.org/W2794917831","https://openalex.org/W2104564563","https://openalex.org/W2013108996","https://openalex.org/W3023224836"],"abstract_inverted_index":{"MOTIVATION:":[0],"Alignment":[1],"of":[2,7,17,23,38,79],"biological":[3],"sequences":[4],"is":[5,36],"one":[6],"the":[8,18,21],"most":[9],"frequently":[10],"performed":[11],"computer":[12],"tasks.":[13],"The":[14],"current":[15],"state":[16],"art":[19],"involves":[20],"use":[22],"(multiple)":[24],"spaced":[25],"seeds":[26,40,55,71],"for":[27,51],"producing":[28],"high":[29,43],"quality":[30],"alignments.":[31],"A":[32],"particular":[33],"important":[34],"class":[35],"that":[37,67],"neighbor":[39,54,70],"which":[41],"combine":[42],"sensitivity":[44],"with":[45],"reduced":[46],"space":[47],"requirements.":[48],"Current":[49],"algorithms":[50],"computing":[52],"good":[53],"are":[56],"very":[57],"slow":[58],"(exponential).":[59],"RESULTS:":[60],"We":[61],"give":[62],"a":[63],"polynomial-time":[64],"heuristic":[65],"algorithm":[66],"computes":[68],"better":[69],"than":[72],"previous":[73],"ones":[74],"while":[75],"being":[76],"several":[77],"orders":[78],"magnitude":[80],"faster.":[81]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
