{"id":"https://openalex.org/W2137458297","doi":"https://doi.org/10.1093/nar/gkg525","title":"PromH: promoters identification using orthologous genomic sequences","display_name":"PromH: promoters identification using orthologous genomic sequences","publication_year":2003,"publication_date":"2003-06-25","ids":{"openalex":"https://openalex.org/W2137458297","doi":"https://doi.org/10.1093/nar/gkg525","mag":"2137458297","pmid":"https://pubmed.ncbi.nlm.nih.gov/12824362"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkg525","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg525","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3540/9487171/gkg525.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","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/nar/article-pdf/31/13/3540/9487171/gkg525.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019821677","display_name":"Victor Solovyev","orcid":"https://orcid.org/0000-0001-8885-493X"},"institutions":[{"id":"https://openalex.org/I4210140806","display_name":"Northern Westchester Hospital","ror":"https://ror.org/05540q762","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1302444339","https://openalex.org/I4210140806"]},{"id":"https://openalex.org/I173210334","display_name":"Newberry College","ror":"https://ror.org/0577pn814","country_code":"US","type":"education","lineage":["https://openalex.org/I173210334"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"V. Solovyev","raw_affiliation_strings":["Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY 10549, USA. victor@softberry.com","Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY 10549, USA"],"affiliations":[{"raw_affiliation_string":"Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY 10549, USA. victor@softberry.com","institution_ids":["https://openalex.org/I173210334"]},{"raw_affiliation_string":"Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY 10549, USA","institution_ids":["https://openalex.org/I4210140806"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5019821677"],"corresponding_institution_ids":["https://openalex.org/I173210334","https://openalex.org/I4210140806"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":2.1733,"has_fulltext":false,"cited_by_count":137,"citation_normalized_percentile":{"value":0.87562613,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"31","issue":"13","first_page":"3540","last_page":"3545"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9976999759674072,"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":0.9965999722480774,"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/promoter","display_name":"Promoter","score":0.871666431427002},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.8498754501342773},{"id":"https://openalex.org/keywords/tata-box","display_name":"TATA box","score":0.7449796795845032},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.7207814455032349},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.7098066806793213},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.5419254302978516},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.5089559555053711},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48880741000175476},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4141693115234375},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.2906057834625244},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.22450211644172668},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.09066352248191833}],"concepts":[{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.871666431427002},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8498754501342773},{"id":"https://openalex.org/C65888428","wikidata":"https://www.wikidata.org/wiki/Q1413955","display_name":"TATA box","level":5,"score":0.7449796795845032},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.7207814455032349},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.7098066806793213},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.5419254302978516},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.5089559555053711},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48880741000175476},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4141693115234375},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.2906057834625244},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.22450211644172668},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.09066352248191833}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":13,"locations":[{"id":"doi:10.1093/nar/gkg525","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg525","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3540/9487171/gkg525.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:12824362","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12824362","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.324.5956","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.324.5956","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/31/13/3540.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:158806","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC168932","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168932","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168932","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/168932","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:repository.royalholloway.ac.uk:49abe871-58ab-40da-b8b0-0bbf6275c8d2/1","is_oa":false,"landing_page_url":"https://repository.royalholloway.ac.uk/items/49abe871-58ab-40da-b8b0-0bbf6275c8d2/1/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401976","display_name":"Royal Holloway Digital Repository (University of London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I166337079","host_organization_name":"Queen Mary University of London","host_organization_lineage":["https://openalex.org/I166337079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 31 (13)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:repository.royalholloway.ac.uk:49abe871-58ab-40da-b8b0-0bbf6275c8d2/2","is_oa":false,"landing_page_url":"https://repository.royalholloway.ac.uk/items/49abe871-58ab-40da-b8b0-0bbf6275c8d2/2/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401976","display_name":"Royal Holloway Digital Repository (University of London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I166337079","host_organization_name":"Queen Mary University of London","host_organization_lineage":["https://openalex.org/I166337079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 31 (13)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:repository.royalholloway.ac.uk:49abe871-58ab-40da-b8b0-0bbf6275c8d2/3","is_oa":false,"landing_page_url":"https://repository.royalholloway.ac.uk/items/49abe871-58ab-40da-b8b0-0bbf6275c8d2/3/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401976","display_name":"Royal Holloway Digital Repository (University of London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I166337079","host_organization_name":"Queen Mary University of London","host_organization_lineage":["https://openalex.org/I166337079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 31 (13)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:repository.royalholloway.ac.uk:49abe871-58ab-40da-b8b0-0bbf6275c8d2/4","is_oa":false,"landing_page_url":"https://repository.royalholloway.ac.uk/items/49abe871-58ab-40da-b8b0-0bbf6275c8d2/4/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401062","display_name":"Royal Holloway Digital Repository (Royal Holloway University of London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184558857","host_organization_name":"Royal Holloway University of London","host_organization_lineage":["https://openalex.org/I184558857"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 31 (13)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:repository.royalholloway.ac.uk:49abe871-58ab-40da-b8b0-0bbf6275c8d2/5","is_oa":false,"landing_page_url":"https://repository.royalholloway.ac.uk/items/49abe871-58ab-40da-b8b0-0bbf6275c8d2/5/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401062","display_name":"Royal Holloway Digital Repository (Royal Holloway University of London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184558857","host_organization_name":"Royal Holloway University of London","host_organization_lineage":["https://openalex.org/I184558857"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 31 (13)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:repository.royalholloway.ac.uk:49abe871-58ab-40da-b8b0-0bbf6275c8d2/6","is_oa":false,"landing_page_url":"https://repository.royalholloway.ac.uk/items/49abe871-58ab-40da-b8b0-0bbf6275c8d2/6/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401062","display_name":"Royal Holloway Digital Repository (Royal Holloway University of London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184558857","host_organization_name":"Royal Holloway University of London","host_organization_lineage":["https://openalex.org/I184558857"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 31 (13)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:repository.royalholloway.ac.uk:49abe871-58ab-40da-b8b0-0bbf6275c8d2/8","is_oa":false,"landing_page_url":"https://repository.royalholloway.ac.uk/items/49abe871-58ab-40da-b8b0-0bbf6275c8d2/8/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401062","display_name":"Royal Holloway Digital Repository (Royal Holloway University of London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184558857","host_organization_name":"Royal Holloway University of London","host_organization_lineage":["https://openalex.org/I184558857"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 31 (13)","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkg525","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg525","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3540/9487171/gkg525.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.44999998807907104,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2137458297.pdf","grobid_xml":"https://content.openalex.org/works/W2137458297.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1501256908","https://openalex.org/W1964007348","https://openalex.org/W1978198515","https://openalex.org/W1980854129","https://openalex.org/W1981800986","https://openalex.org/W2003463914","https://openalex.org/W2008900336","https://openalex.org/W2011282682","https://openalex.org/W2072032642","https://openalex.org/W2096329971","https://openalex.org/W2101633713","https://openalex.org/W2101690350","https://openalex.org/W2104730528","https://openalex.org/W2106756765","https://openalex.org/W2113197426","https://openalex.org/W2124195715","https://openalex.org/W2124220434","https://openalex.org/W2124332179","https://openalex.org/W2139516179","https://openalex.org/W2142890842","https://openalex.org/W2151464048","https://openalex.org/W2169351355","https://openalex.org/W4242043490"],"related_works":["https://openalex.org/W2134002428","https://openalex.org/W1989509859","https://openalex.org/W1991259976","https://openalex.org/W3163988421","https://openalex.org/W4245957168","https://openalex.org/W186167790","https://openalex.org/W1871847816","https://openalex.org/W2133676917","https://openalex.org/W1993786842","https://openalex.org/W2129029591"],"abstract_inverted_index":{"Accurate":[0],"prediction":[1,262],"of":[2,18,21,24,93,98,108,110,149,157,233,237],"promoters":[3,185],"is":[4,267],"fundamental":[5],"for":[6,145,165,193,221],"understanding":[7],"gene":[8],"expression":[9],"patterns,":[10],"cell":[11],"specificity":[12],"and":[13,41,90,114,132,172,178,206,218],"development.":[14],"In":[15,243],"the":[16,49,74,150,187,224],"studies":[17],"conserved":[19],"features":[20,89],"regulatory":[22,42],"regions":[23,95],"orthologous":[25,99,130],"genes,":[26,128,135,167,195],"it":[27],"was":[28,103,168,191],"observed":[29],"that":[30,84,249],"major":[31],"promoter":[32,59,94,261],"functional":[33],"components":[34],"such":[35],"as":[36],"transcription":[37,119],"start":[38,120],"points,":[39],"TATA-boxes":[40],"motifs,":[43],"are":[44,229],"significantly":[45,254],"more":[46,214,255],"conservative":[47],"than":[48,257],"sequences":[50,92,116],"around":[51],"them":[52],"(70-100%":[53],"compared":[54],"with":[55,117,153,231],"30-50%).":[56],"To":[57],"improve":[58],"identification":[60],"accuracy,":[61],"we":[62],"employed":[63],"these":[64,227],"findings":[65],"in":[66,96,196,207,240],"a":[67,154],"new":[68],"program,":[69],"PromH,":[70],"created":[71],"by":[72],"extending":[73],"TSSW":[75],"program":[76,102,141,266],"feature":[77],"set.":[78],"PromH":[79,250,265],"uses":[80],"linear":[81],"discriminant":[82],"functions":[83],"take":[85],"into":[86],"account":[87],"conservation":[88],"nucleotide":[91],"pairs":[97,109],"genes.":[100],"The":[101,140,264],"tested":[104],"on":[105],"two":[106,166],"sets":[107],"orthologous,":[111],"mostly":[112],"human":[113],"rodent,":[115],"known":[118],"sites":[121],"(TSS),":[122],"annotated":[123,179,204,219],"to":[124],"have":[125],"TATA":[126],"(21":[127],"11":[129],"pairs)":[131,137],"TATA-less":[133,184,241],"(38":[134],"19":[136],"promoters,":[138],"respectively.":[139],"correctly":[142],"predicted":[143,177,192,217],"TSS":[144,180,190,220,239,252],"all":[146],"21":[147,208],"genes":[148,222],"first":[151],"set":[152],"median":[155],"deviation":[156],"2":[158],"bp":[159,201,211],"from":[160,186,203,223],"true":[161],"site":[162],"location.":[163],"Only":[164],"there":[169],"significant":[170],"(46":[171],"105":[173],"bp)":[174],"discrepancy":[175],"between":[176,216],"positions.":[181],"For":[182],"38":[183],"second":[188,225],"set,":[189,226],"27":[194],"14":[197],"cases":[198],"within":[199],"10":[200],"distance":[202],"TSS,":[205],"cases--within":[209],"100":[210],"distance.":[212],"Despite":[213],"discrepancies":[215],"results":[228,247],"consistent":[230],"observations":[232],"much":[234],"higher":[235],"occurrence":[236],"multiple":[238],"promoters.":[242],"any":[244,258],"case,":[245],"our":[246],"show":[248],"identifies":[251],"positions":[253],"accurately":[256],"other":[259],"published":[260],"method.":[263],"available":[268],"at":[269],"http://www.softberry.com/berry.phtml?topic=promh.":[270]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
