{"id":"https://openalex.org/W2146231163","doi":"https://doi.org/10.1186/1748-7188-5-15","title":"Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data","display_name":"Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data","publication_year":2010,"publication_date":"2010-01-26","ids":{"openalex":"https://openalex.org/W2146231163","doi":"https://doi.org/10.1186/1748-7188-5-15","mag":"2146231163","pmid":"https://pubmed.ncbi.nlm.nih.gov/20205909"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-5-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-15","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-15","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-15","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109225913","display_name":"Gr\u00e9gory Nuel","orcid":null},"institutions":[{"id":"https://openalex.org/I110736937","display_name":"D\u00e9l\u00e9gation Paris 5","ror":"https://ror.org/02e0y6e06","country_code":"FR","type":"government","lineage":["https://openalex.org/I110736937","https://openalex.org/I154526488"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4387154995","display_name":"Math\u00e9matiques Appliqu\u00e9es \u00e0 Paris 5","ror":"https://ror.org/04yrrdj53","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4387154995"]},{"id":"https://openalex.org/I88467170","display_name":"Universit\u00e9 d'\u00c9vry Val-d'Essonne","ror":"https://ror.org/00e96v939","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Gregory Nuel","raw_affiliation_strings":["CNRS, Paris, France","LSG, Laboratoire Statistique et G\u00e9nome, CNRS UMR-8071, INRA UMR-1152, University of Evry, Evry, France","MAP5, Department of Applied Mathematics, CNRS UMR-8145, University Paris Descartes, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNRS, Paris, France","institution_ids":["https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LSG, Laboratoire Statistique et G\u00e9nome, CNRS UMR-8071, INRA UMR-1152, University of Evry, Evry, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I88467170"]},{"raw_affiliation_string":"MAP5, Department of Applied Mathematics, CNRS UMR-8145, University Paris Descartes, Paris, France","institution_ids":["https://openalex.org/I110736937","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4387154995"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066913640","display_name":"Leslie Regad","orcid":"https://orcid.org/0000-0002-9292-5283"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Leslie Regad","raw_affiliation_strings":["EBGM, Equipe de Bioinformatique G\u00e9nomique et Moleculaire, INSERM UMRS-726, University Paris Diderot, Paris, France","MTi, Molecules Th\u00e9rapeutique in silico, INSERM UMRS-973, University Paris Diderot, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EBGM, Equipe de Bioinformatique G\u00e9nomique et Moleculaire, INSERM UMRS-726, University Paris Diderot, Paris, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241"]},{"raw_affiliation_string":"MTi, Molecules Th\u00e9rapeutique in silico, INSERM UMRS-973, University Paris Diderot, Paris, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I169173203","https://openalex.org/I204730241"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026973395","display_name":"Juliette Martin","orcid":"https://orcid.org/0000-0002-4787-0885"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210087293","display_name":"Institut de Biologie et de Chimie des Prot\u00e9ines","ror":"https://ror.org/0019x5d05","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I4210087293","https://openalex.org/I4210096427"]},{"id":"https://openalex.org/I4210159481","display_name":"Math\u00e9matiques et Informatique Appliqu\u00e9es du G\u00e9nome \u00e0 l'Environnement","ror":"https://ror.org/05qdnns64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210159481"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Juliette Martin","raw_affiliation_strings":["EBGM, Equipe de Bioinformatique G\u00e9nomique et Moleculaire, INSERM UMRS-726, University Paris Diderot, Paris, France","IBCP, Institut de Biologie et Chimie des Prot\u00e9ines, IFR 128, CNRS UMR 5086, University of Lyon 1, Lyon, France","MIG, Math\u00e9matique Informatique et Genome, INRA UR-1077, Jouy-en-Josas, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EBGM, Equipe de Bioinformatique G\u00e9nomique et Moleculaire, INSERM UMRS-726, University Paris Diderot, Paris, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241"]},{"raw_affiliation_string":"IBCP, Institut de Biologie et Chimie des Prot\u00e9ines, IFR 128, CNRS UMR 5086, University of Lyon 1, Lyon, France","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I4210087293"]},{"raw_affiliation_string":"MIG, Math\u00e9matique Informatique et Genome, INRA UR-1077, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I4210159481"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015097541","display_name":"Anne\u2010Claude Camproux","orcid":"https://orcid.org/0000-0001-8821-9952"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I169173203","display_name":"D\u00e9l\u00e9gation Paris 7","ror":"https://ror.org/00bw5n526","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488","https://openalex.org/I169173203"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anne-Claude Camproux","raw_affiliation_strings":["EBGM, Equipe de Bioinformatique G\u00e9nomique et Moleculaire, INSERM UMRS-726, University Paris Diderot, Paris, France","MTi, Molecules Th\u00e9rapeutique in silico, INSERM UMRS-973, University Paris Diderot, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EBGM, Equipe de Bioinformatique G\u00e9nomique et Moleculaire, INSERM UMRS-726, University Paris Diderot, Paris, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I204730241"]},{"raw_affiliation_string":"MTi, Molecules Th\u00e9rapeutique in silico, INSERM UMRS-973, University Paris Diderot, Paris, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I169173203","https://openalex.org/I204730241"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5109225913"],"corresponding_institution_ids":["https://openalex.org/I110736937","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4387154995","https://openalex.org/I88467170"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":1.4942,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.81600586,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"5","issue":"1","first_page":"15","last_page":"15"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.19120000302791595,"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/T10885","display_name":"Gene expression and cancer classification","score":0.19120000302791595,"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":0.14569999277591705,"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":0.09610000252723694,"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/computer-science","display_name":"Computer science","score":0.7019489407539368},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5080482959747314},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.4831378161907196},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.44535213708877563},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.4116441011428833},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.37700092792510986},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16088587045669556},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.13106587529182434}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7019489407539368},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5080482959747314},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.4831378161907196},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.44535213708877563},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.4116441011428833},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.37700092792510986},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16088587045669556},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.13106587529182434}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1748-7188-5-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-15","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-15","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:20205909","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20205909","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:europepmc.org:1909181","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2828453","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:HAL:inserm-00663534v1","is_oa":true,"landing_page_url":"https://inserm.hal.science/inserm-00663534","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, 2010, 5 (1), pp.15. &#x27E8;10.1186/1748-7188-5-15&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:0fe2c746906a49949c922554262b4b5d","is_oa":false,"landing_page_url":"https://doaj.org/article/0fe2c746906a49949c922554262b4b5d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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":"Algorithms for Molecular Biology, Vol 5, Iss 1, p 15 (2010)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-5-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-5-15","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-5-15","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2146231163.pdf","grobid_xml":"https://content.openalex.org/works/W2146231163.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W82544137","https://openalex.org/W1533513619","https://openalex.org/W1566314357","https://openalex.org/W1964344408","https://openalex.org/W1967699304","https://openalex.org/W1971912858","https://openalex.org/W1980260642","https://openalex.org/W1998203805","https://openalex.org/W2002089154","https://openalex.org/W2002220902","https://openalex.org/W2018983027","https://openalex.org/W2024299495","https://openalex.org/W2027922789","https://openalex.org/W2035927204","https://openalex.org/W2038088862","https://openalex.org/W2050322157","https://openalex.org/W2053272249","https://openalex.org/W2053392780","https://openalex.org/W2054274631","https://openalex.org/W2060354467","https://openalex.org/W2060418270","https://openalex.org/W2063004022","https://openalex.org/W2067615780","https://openalex.org/W2077299429","https://openalex.org/W2078010999","https://openalex.org/W2081523148","https://openalex.org/W2084082653","https://openalex.org/W2085073388","https://openalex.org/W2088082060","https://openalex.org/W2088281350","https://openalex.org/W2099182237","https://openalex.org/W2099800150","https://openalex.org/W2101386484","https://openalex.org/W2107768450","https://openalex.org/W2107966552","https://openalex.org/W2110519987","https://openalex.org/W2111329690","https://openalex.org/W2119478675","https://openalex.org/W2125723560","https://openalex.org/W2130956021","https://openalex.org/W2136292095","https://openalex.org/W2149769193","https://openalex.org/W2157485293","https://openalex.org/W2159507861","https://openalex.org/W2159862550","https://openalex.org/W2161062388","https://openalex.org/W2163781727","https://openalex.org/W2169016544","https://openalex.org/W2213701196","https://openalex.org/W2225480587","https://openalex.org/W2317416722","https://openalex.org/W2326525345","https://openalex.org/W2506088122","https://openalex.org/W2912570624","https://openalex.org/W2915868289","https://openalex.org/W2951868424","https://openalex.org/W3100779835","https://openalex.org/W3105867654","https://openalex.org/W3145366215","https://openalex.org/W4211000692","https://openalex.org/W4212865600","https://openalex.org/W4254811854","https://openalex.org/W4285719527","https://openalex.org/W4296472334","https://openalex.org/W4298365428","https://openalex.org/W4300505472"],"related_works":["https://openalex.org/W2053269318","https://openalex.org/W2364370872","https://openalex.org/W2097963413","https://openalex.org/W2025614924","https://openalex.org/W2294335174","https://openalex.org/W3145575561","https://openalex.org/W2995886640","https://openalex.org/W1591475660","https://openalex.org/W2001275470","https://openalex.org/W2164162849"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1,182,318],"bioinformatics":[2],"it":[3],"is":[4,130],"common":[5],"to":[6,34,70,80,109,123,135,143,176,200,206,264,286,291,325,338],"search":[7],"for":[8,85,316],"a":[9,14,39,43,48,63,111,164,207,228,244,279,311,350,361],"pattern":[10,40,151],"of":[11,18,38,60,65,94,113,147,149,173,186,304,346],"interest":[12,216],"in":[13,42,62,91,104,153,167,217,237,243,250,270,274],"potentially":[15],"large":[16],"set":[17,64,277],"rather":[19],"short":[20],"sequences":[21,273],"(upstream":[22],"gene":[23,252],"regions,":[24],"proteins,":[25],"exons,":[26],"etc.).":[27],"Although":[28],"many":[29],"methodological":[30],"approaches":[31,77,263],"allow":[32,323],"practitioners":[33],"compute":[35],"the":[36,58,92,105,131,150,168,183,203,265,272,275,308,327,332,343,347,354],"distribution":[37,152,345],"count":[41],"random":[44],"sequence":[45,334],"generated":[46],"by":[47,74,170],"Markov":[49,98,115],"source,":[50],"no":[51],"specific":[52],"developments":[53],"have":[54],"taken":[55],"into":[56,278],"account":[57],"counting":[59],"occurrences":[61],"independent":[66],"sequences.":[67,155],"We":[68,357],"aim":[69],"address":[71],"this":[72],"problem":[73],"deriving":[75],"efficient":[76],"and":[78,87,197,213,225,230,247,289,366],"algorithms":[79,212,284,322],"perform":[81],"these":[82,211,255,320],"computations":[83,175],"both":[84],"low":[86,187],"high":[88,312],"complexity":[89,169,190,205,313],"patterns":[90,236,303],"framework":[93],"homogeneous":[95,159],"or":[96,188],"heterogeneous":[97,138],"models.":[99,139],"RESULTS:":[100],"The":[101],"latest":[102],"advances":[103],"field":[106],"allowed":[107],"us":[108,324],"use":[110],"technique":[112],"optimal":[114],"chain":[116],"embedding":[117],"based":[118],"on":[119,227,363,367],"deterministic":[120],"finite":[121],"automata":[122],"introduce":[124],"three":[125,231],"innovative":[126],"algorithms.":[127],"Algorithm":[128,161,192],"1":[129],"only":[132],"one":[133],"able":[134,290],"deal":[136],"with":[137,158,219,296,360],"It":[140],"also":[141,259],"permits":[142],"avoid":[144,326],"any":[145],"product":[146],"convolution":[148],"individual":[154],"When":[156],"working":[157],"models,":[160],"2":[162],"yields":[163],"dramatic":[165],"reduction":[166],"taking":[171],"advantage":[172],"previous":[174],"obtain":[177],"moment":[178],"generating":[179],"functions":[180],"efficiently.":[181],"particular":[184],"case":[185],"moderate":[189],"patterns,":[191],"3":[193],"exploits":[194],"power":[195],"computation":[196],"binary":[198],"decomposition":[199],"further":[201],"reduce":[202],"time":[204],"logarithmic":[208],"scale.":[209],"All":[210],"their":[214],"relative":[215],"comparison":[218],"existing":[220],"ones":[221],"were":[222],"then":[223],"tested":[224],"discussed":[226],"toy-example":[229],"biological":[232,302],"data":[233,256,276,294],"sets:":[234],"structural":[235],"protein":[238],"loop":[239],"structures,":[240],"PROSITE":[241],"signatures":[242,315],"bacterial":[245],"proteome,":[246],"transcription":[248],"factors":[249],"upstream":[251],"regions.":[253],"On":[254],"sets,":[257],"we":[258],"compared":[260],"our":[261,364],"exact":[262,321],"tempting":[266],"approximation":[267],"that":[268],"consists":[269],"concatenating":[271],"single":[280,333],"sequence.":[281],"CONCLUSIONS:":[282],"Our":[283],"prove":[285],"be":[287],"effective":[288],"handle":[292],"real":[293],"sets":[295],"multiple":[297],"sequences,":[298],"as":[299,301],"well":[300],"interest,":[305],"even":[306],"when":[307,342],"latter":[309],"display":[310],"(PROSITE":[314],"example).":[317],"addition,":[319],"edge":[328],"effect":[329],"observed":[330],"under":[331],"approximation,":[335],"which":[336],"leads":[337],"erroneous":[339],"results,":[340],"especially":[341],"marginal":[344],"model":[348],"displays":[349],"slow":[351],"convergence":[352],"toward":[353],"stationary":[355],"distribution.":[356],"end":[358],"up":[359],"discussion":[362],"method":[365],"its":[368],"potential":[369],"improvements.":[370]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
