{"id":"https://openalex.org/W1997199912","doi":"https://doi.org/10.1016/s0097-8485(96)80003-9","title":"A flexible motif search technique based on generalized profiles","display_name":"A flexible motif search technique based on generalized profiles","publication_year":1996,"publication_date":"1996-03-01","ids":{"openalex":"https://openalex.org/W1997199912","doi":"https://doi.org/10.1016/s0097-8485(96)80003-9","mag":"1997199912","pmid":"https://pubmed.ncbi.nlm.nih.gov/8867839"},"language":"en","primary_location":{"id":"doi:10.1016/s0097-8485(96)80003-9","doi":"https://doi.org/10.1016/s0097-8485(96)80003-9","is_oa":false,"landing_page_url":"https://doi.org/10.1016/s0097-8485(96)80003-9","pdf_url":null,"source":{"id":"https://openalex.org/S4210194753","display_name":"Computers & Chemistry","issn_l":"0097-8485","issn":["0097-8485","1879-0763"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","norway-1"],"host_organization":"https://openalex.org/P4310320146","host_organization_name":"Pergamon Press","host_organization_lineage":["https://openalex.org/P4310320146"],"host_organization_lineage_names":["Pergamon Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computers & Chemistry","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://infoscience.epfl.ch/record/77235","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103270230","display_name":"Philipp B\u00fccher","orcid":"https://orcid.org/0000-0003-4824-885X","observed_orcids":["https://orcid.org/0000-0003-4824-885X","https://orcid.org/0000-0003-4276-9419"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Philipp Bucher","raw_affiliation_strings":["Swiss Institute for Experimental Cancer Research, Epalinges, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Swiss Institute for Experimental Cancer Research, Epalinges, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059033237","display_name":"Kevin J. Karplus","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin Karplus","raw_affiliation_strings":["Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, U.S.A"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, U.S.A","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089697484","display_name":"Nicolas Moeri","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Nicolas Moeri","raw_affiliation_strings":["D\u00e9partement de Math\u00e9matiques, Ecole Polytechnique F\u00e9d\u00e9rale, CH-1015 Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement de Math\u00e9matiques, Ecole Polytechnique F\u00e9d\u00e9rale, CH-1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103095154","display_name":"Kay Hofmann","orcid":"https://orcid.org/0000-0002-2289-9083","observed_orcids":["https://orcid.org/0000-0002-2289-9083"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kay Hofmann","raw_affiliation_strings":["Swiss Institute for Experimental Cancer Research, CH-1066 Epalinges, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Swiss Institute for Experimental Cancer Research, CH-1066 Epalinges, Switzerland","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":6.4199,"has_fulltext":false,"cited_by_count":316,"citation_normalized_percentile":{"value":0.97492966,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"20","issue":"1","first_page":"3","last_page":"23"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5889000296592712,"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":0.5889000296592712,"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":0.27469998598098755,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.041600000113248825,"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/motif-search","display_name":"motif search","score":0.878000020980835},{"id":"https://openalex.org/keywords/sequence-motifs","display_name":"sequence motifs","score":0.41999998688697815},{"id":"https://openalex.org/keywords/hidden-markov-models","display_name":"hidden Markov models","score":0.906000018119812},{"id":"https://openalex.org/keywords/weighting-matrix","display_name":"weight matrix","score":0.8479999899864197},{"id":"https://openalex.org/keywords/local-sequence-alignment","display_name":"local alignment","score":0.6230000257492065},{"id":"https://openalex.org/keywords/stochastic-modeling","display_name":"stochastic modeling","score":0.7319999933242798},{"id":"https://openalex.org/keywords/significance-tests","display_name":"significance tests","score":0.7039999961853027}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.8070996999740601},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5377028584480286},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.4369157552719116},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.43220943212509155},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.413998544216156},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4117129147052765},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.34890443086624146},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34666723012924194},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.308631032705307},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.12696710228919983},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.06515142321586609},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005914","descriptor_name":"Globins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017475","descriptor_name":"Receptors, Nerve Growth Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018124","descriptor_name":"Receptors, Tumor Necrosis Factor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1016/s0097-8485(96)80003-9","doi":"https://doi.org/10.1016/s0097-8485(96)80003-9","is_oa":false,"landing_page_url":"https://doi.org/10.1016/s0097-8485(96)80003-9","pdf_url":null,"source":{"id":"https://openalex.org/S4210194753","display_name":"Computers & Chemistry","issn_l":"0097-8485","issn":["0097-8485","1879-0763"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","norway-1"],"host_organization":"https://openalex.org/P4310320146","host_organization_name":"Pergamon Press","host_organization_lineage":["https://openalex.org/P4310320146"],"host_organization_lineage_names":["Pergamon Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computers & Chemistry","raw_type":"journal-article"},{"id":"pmid:8867839","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/8867839","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,"listed_in":[],"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":"Computers & chemistry","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.144.8809","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.144.8809","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cse.ucsc.edu/~karplus/papers/generalized-profile-1996.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.44.5710","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.44.5710","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cse.ucsc.edu//research/compbio/papers/generalized-profile.ps.gz","raw_type":"text"},{"id":"pmh:oai:infoscience.epfl.ch:77235","doi":null,"is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/77235","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I5124864","host_organization_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","host_organization_lineage":["https://openalex.org/I5124864"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:infoscience.tind.io:77235","doi":null,"is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/77235","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I5124864","host_organization_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","host_organization_lineage":["https://openalex.org/I5124864"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"research article"},{"id":"pmh:oai:iris.unil.ch:iris/98756","doi":null,"is_oa":false,"landing_page_url":"https://iris.unil.ch/handle/iris/98756","pdf_url":null,"source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":null,"raw_type":"journal article"},{"id":"pmh:oai:serval.unil.ch:BIB_4543","doi":null,"is_oa":false,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_4543","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Comp Chem, vol. 20, pp. 3-24","raw_type":"info:eu-repo/semantics/article"},{"id":"mag:3013207870","doi":null,"is_oa":false,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_4543","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:infoscience.epfl.ch:77235","doi":null,"is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/77235","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I5124864","host_organization_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","host_organization_lineage":["https://openalex.org/I5124864"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1422803820","https://openalex.org/W1558365920","https://openalex.org/W1565582771","https://openalex.org/W1599577927","https://openalex.org/W1969051510","https://openalex.org/W1969451865","https://openalex.org/W1973578915","https://openalex.org/W1977618577","https://openalex.org/W1987680287","https://openalex.org/W2002640757","https://openalex.org/W2008841836","https://openalex.org/W2011495938","https://openalex.org/W2013490745","https://openalex.org/W2013570924","https://openalex.org/W2023206235","https://openalex.org/W2031121939","https://openalex.org/W2035564383","https://openalex.org/W2044966609","https://openalex.org/W2054698853","https://openalex.org/W2054849588","https://openalex.org/W2056415332","https://openalex.org/W2056574818","https://openalex.org/W2066513603","https://openalex.org/W2074231493","https://openalex.org/W2078071124","https://openalex.org/W2099180682","https://openalex.org/W2102122585","https://openalex.org/W2106882534","https://openalex.org/W2125838338","https://openalex.org/W2143210482","https://openalex.org/W4246356731"],"related_works":["https://openalex.org/W1533208683","https://openalex.org/W7098265802","https://openalex.org/W102281645","https://openalex.org/W1660760521","https://openalex.org/W2151831732","https://openalex.org/W2123446746","https://openalex.org/W2025325736","https://openalex.org/W2001365663","https://openalex.org/W2080681386","https://openalex.org/W2145445013"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":9}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}