{"id":"https://openalex.org/W2101843343","doi":"https://doi.org/10.1093/bioinformatics/btf872","title":"MELINA: motif extraction from promoter regions of potentially co-regulated genes","display_name":"MELINA: motif extraction from promoter regions of potentially co-regulated genes","publication_year":2003,"publication_date":"2003-02-12","ids":{"openalex":"https://openalex.org/W2101843343","doi":"https://doi.org/10.1093/bioinformatics/btf872","mag":"2101843343","pmid":"https://pubmed.ncbi.nlm.nih.gov/12584132"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btf872","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btf872","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/423/48903780/bioinformatics_19_3_423.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/19/3/423/48903780/bioinformatics_19_3_423.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080393700","display_name":"Natalia Poluliakh","orcid":null},"institutions":[{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Natalia Poluliakh","raw_affiliation_strings":["Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan","Human Genome Center, Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku Tokyo 108-8639 Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan","institution_ids":["https://openalex.org/I161296585","https://openalex.org/I74801974"]},{"raw_affiliation_string":"Human Genome Center, Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku Tokyo 108-8639 Japan","institution_ids":["https://openalex.org/I161296585","https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104355283","display_name":"Toshihisa Takagi","orcid":null},"institutions":[{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Toshihisa Takagi","raw_affiliation_strings":["Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan and","institution_ids":["https://openalex.org/I161296585","https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054681585","display_name":"Kenta Nakai","orcid":"https://orcid.org/0000-0002-8721-8883"},"institutions":[{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kenta Nakai","raw_affiliation_strings":["Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan and","university of Tokyo;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan and","institution_ids":["https://openalex.org/I161296585","https://openalex.org/I74801974"]},{"raw_affiliation_string":"university of Tokyo;","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9754,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.73260335,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"19","issue":"3","first_page":"423","last_page":"424"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9988999962806702,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9988999962806702,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9902999997138977,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.984000027179718,"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/motif","display_name":"Motif (music)","score":0.7978907823562622},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5239520072937012},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4780843257904053},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4200163781642914},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.41653889417648315},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.40914565324783325},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39862772822380066},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3090304434299469},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24990373849868774}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7978907823562622},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5239520072937012},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4780843257904053},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4200163781642914},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.41653889417648315},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.40914565324783325},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39862772822380066},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3090304434299469},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24990373849868774},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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":"D016415","descriptor_name":"Sequence Alignment","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btf872","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btf872","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/423/48903780/bioinformatics_19_3_423.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:12584132","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12584132","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:10.1.1.623.3654","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.623.3654","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/19/3/423.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btf872","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btf872","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/423/48903780/bioinformatics_19_3_423.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":[{"id":"https://metadata.un.org/sdg/17","score":0.4699999988079071,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2101843343.pdf","grobid_xml":"https://content.openalex.org/works/W2101843343.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1592870802","https://openalex.org/W1975924111","https://openalex.org/W1990762432","https://openalex.org/W1998300401","https://openalex.org/W2149769193","https://openalex.org/W2162600254"],"related_works":["https://openalex.org/W2073661767","https://openalex.org/W2143211236","https://openalex.org/W2380185347","https://openalex.org/W2370034659","https://openalex.org/W2159636084","https://openalex.org/W2610941444","https://openalex.org/W2117168988","https://openalex.org/W2154430121","https://openalex.org/W2103777723","https://openalex.org/W2605190264"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"\u2018Melina\u2019":[2],"assists":[3],"users":[4],"to":[5,19,36],"compare":[6],"the":[7,22,38],"results":[8],"of":[9,24,40,45],"four":[10],"public":[11],"softwares":[12],"for":[13],"DNA":[14],"motif":[15],"extraction":[16],"in":[17],"order":[18],"both":[20],"confirm":[21],"reliability":[23],"each":[25],"finding":[26],"and":[27],"avoid":[28],"missing":[29],"important":[30],"motifs.":[31],"It":[32],"is":[33,51],"also":[34],"useful":[35],"optimize":[37],"sensitivity":[39],"software":[41],"with":[42],"a":[43],"series":[44],"different":[46],"parameter":[47],"settings.":[48],"Availability:":[49],"Melina":[50],"available":[52],"at":[53],"http://www.hgc.ims.u-tokyo.ac.jp/Melina/":[54],"Contact:":[55],"knakai@ims.u-tokyo.ac.jp":[56],"*":[57],"To":[58],"whom":[59],"correspondence":[60],"should":[61],"be":[62],"addressed.":[63]},"counts_by_year":[{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
