{"id":"https://openalex.org/W2129782019","doi":"https://doi.org/10.1109/bibe.2004.1317368","title":"Good spaced seeds for homology search","display_name":"Good spaced seeds for homology search","publication_year":2004,"publication_date":"2004-11-30","ids":{"openalex":"https://openalex.org/W2129782019","doi":"https://doi.org/10.1109/bibe.2004.1317368","mag":"2129782019"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2004.1317368","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2004.1317368","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5102728558","display_name":"Kwok Pui Choi","orcid":"https://orcid.org/0000-0003-2373-1773"},"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"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Kwok Pui Choi","raw_affiliation_strings":["Department of Mathematics & Department of Statistics and Applied Probability, National University of Singapore, Singapore","Department of Math, National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics & Department of Statistics and Applied Probability, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Department of Math, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027901992","display_name":"Fanfan Zeng","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"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Fanfan Zeng","raw_affiliation_strings":["School of Computing, NUS, Singapore","School of Computing, National University of Singapore, Singapore 117543,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, NUS, Singapore","institution_ids":[]},{"raw_affiliation_string":"School of Computing, National University of Singapore, Singapore 117543,","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012300835","display_name":"Louxin Zhang","orcid":"https://orcid.org/0000-0003-0260-824X"},"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"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Louxin Zhang","raw_affiliation_strings":["Department of Mathematics, NUS, Singapore","National University of Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, NUS, Singapore","institution_ids":[]},{"raw_affiliation_string":"National University of Singapore","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I165932596"],"apc_list":null,"apc_paid":null,"fwci":0.1197,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.49535359,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"1643","issue":null,"first_page":"379","last_page":"386"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9898999929428101,"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/similarity","display_name":"Similarity (geometry)","score":0.6764846444129944},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.625020444393158},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6059946417808533},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.5919844508171082},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5076407194137573},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.45714548230171204},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.44809016585350037},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.4467429220676422},{"id":"https://openalex.org/keywords/genomic-dna","display_name":"genomic DNA","score":0.4231416583061218},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39998558163642883},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3736354112625122},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36235442757606506},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3511272072792053},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.33273887634277344},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.32888883352279663},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32105034589767456},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2525327205657959},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2518959939479828},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1286689043045044},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09804612398147583},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.0659436583518982}],"concepts":[{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6764846444129944},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.625020444393158},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6059946417808533},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.5919844508171082},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5076407194137573},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.45714548230171204},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.44809016585350037},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.4467429220676422},{"id":"https://openalex.org/C17757408","wikidata":"https://www.wikidata.org/wiki/Q4135516","display_name":"genomic DNA","level":3,"score":0.4231416583061218},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39998558163642883},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3736354112625122},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36235442757606506},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3511272072792053},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.33273887634277344},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.32888883352279663},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32105034589767456},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2525327205657959},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2518959939479828},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1286689043045044},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09804612398147583},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0659436583518982},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2004.1317368","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2004.1317368","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320335846","display_name":"Biomedical Research Council","ror":"https://ror.org/03xy0wx88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1482802109","https://openalex.org/W1807142859","https://openalex.org/W1821582542","https://openalex.org/W1873119440","https://openalex.org/W1965280193","https://openalex.org/W1965941177","https://openalex.org/W1972051891","https://openalex.org/W1993158258","https://openalex.org/W2008841836","https://openalex.org/W2024811036","https://openalex.org/W2029195137","https://openalex.org/W2055043387","https://openalex.org/W2055666215","https://openalex.org/W2057998009","https://openalex.org/W2101664494","https://openalex.org/W2109034006","https://openalex.org/W2128591967","https://openalex.org/W2136145671","https://openalex.org/W2141847640","https://openalex.org/W2142619120","https://openalex.org/W2143286856","https://openalex.org/W2148399816","https://openalex.org/W2151464048","https://openalex.org/W2152331922","https://openalex.org/W2158714788","https://openalex.org/W2160802334","https://openalex.org/W2912268188","https://openalex.org/W4236236547","https://openalex.org/W6628896446","https://openalex.org/W6643069710"],"related_works":["https://openalex.org/W2004215917","https://openalex.org/W2948014085","https://openalex.org/W1974956921","https://openalex.org/W2131326525","https://openalex.org/W2139695554","https://openalex.org/W2103737249","https://openalex.org/W1972247471","https://openalex.org/W1486249959","https://openalex.org/W2166325055","https://openalex.org/W2885386129"],"abstract_inverted_index":{"Filtration":[0],"is":[1,58],"an":[2],"important":[3],"technique":[4],"used":[5],"to":[6,37,45],"speed":[7],"up":[8],"local":[9,48],"alignment":[10,49],"as":[11],"exemplified":[12],"in":[13,50,113],"the":[14,33,68,78,90,120],"BLAST":[15],"programs.":[16],"Recently,":[17],"Ma,":[18],"Tromp":[19],"and":[20,101],"Li":[21],"(2002)":[22],"discovered":[23],"that":[24,67,119],"better":[25],"filtering":[26],"can":[27],"be":[28],"achieved":[29],"by":[30],"spacing":[31],"out":[32],"matching":[34],"positions":[35,44],"according":[36],"a":[38,47,55,60,96,103],"certain":[39],"pattern,":[40],"instead":[41],"of":[42,70,92,98,105,133],"contiguous":[43],"trigger":[46],"their":[51],"PatternHunter":[52],"program.":[53],"Such":[54],"match":[56],"pattern":[57],"called":[59],"spaced":[61,71,93,107,122],"seed.":[62],"Our":[63],"numerical":[64],"computation":[65],"shows":[66],"ranks":[69],"seeds":[72,94,108,123],"(based":[73],"on":[74],"sensitivity)":[75],"change":[76],"with":[77],"sequences":[79,83],"similarity.":[80],"Since":[81],"homologous":[82],"may":[84],"have":[85],"diverse":[86],"similarity,":[87],"we":[88],"assess":[89],"sensitivity":[91],"over":[95],"range":[97],"similarity":[99],"levels":[100],"present":[102],"list":[104],"good":[106],"for":[109],"facilitating":[110],"homology":[111],"search":[112],"DNA":[114,134],"genomic":[115,135],"sequences.":[116,136],"We":[117],"validate":[118],"listed":[121],"are":[124],"indeed":[125],"more":[126],"sensitive":[127],"using":[128],"three":[129],"arbitrarily":[130],"chosen":[131],"pairs":[132]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}