{"id":"https://openalex.org/W2119447107","doi":"https://doi.org/10.1093/nar/gkg627","title":"GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives","display_name":"GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives","publication_year":2003,"publication_date":"2003-06-25","ids":{"openalex":"https://openalex.org/W2119447107","doi":"https://doi.org/10.1093/nar/gkg627","mag":"2119447107","pmid":"https://pubmed.ncbi.nlm.nih.gov/12824434"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkg627","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg627","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3843/9487660/gkg627.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/31/13/3843/9487660/gkg627.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089067185","display_name":"Edouard Yeramian","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"E. Yeramian","raw_affiliation_strings":["Unit\u00e9 de Bio-Informatique Structurale, URA CNRS 2185, Institut Pasteur, 75724 Paris Cedex 15, France. yeramian@pasteur.fr","Unit\u00e9 de Bio-Informatique Structurale, URA CNRS 2185, Institut Pasteur, 75724 Paris Cedex 15, France"],"affiliations":[{"raw_affiliation_string":"Unit\u00e9 de Bio-Informatique Structurale, URA CNRS 2185, Institut Pasteur, 75724 Paris Cedex 15, France. yeramian@pasteur.fr","institution_ids":["https://openalex.org/I157536573","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Unit\u00e9 de Bio-Informatique Structurale, URA CNRS 2185, Institut Pasteur, 75724 Paris Cedex 15, France","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5089067185"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I157536573"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":1.2207,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.77734569,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"31","issue":"13","first_page":"3843","last_page":"3849"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10521","display_name":"RNA and protein synthesis mechanisms","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":0.9983000159263611,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9941999912261963,"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/biology","display_name":"Biology","score":0.7764582633972168},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.6029411554336548},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5909581184387207},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5751590728759766},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.527005136013031},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.5123790502548218},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4855756163597107},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4368024468421936},{"id":"https://openalex.org/keywords/coding-region","display_name":"Coding region","score":0.42409706115722656},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21509835124015808},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.19083696603775024}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7764582633972168},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.6029411554336548},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5909581184387207},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5751590728759766},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.527005136013031},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.5123790502548218},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4855756163597107},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4368024468421936},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.42409706115722656},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21509835124015808},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.19083696603775024},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005815","descriptor_name":"Genetic Code","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010963","descriptor_name":"Plasmodium falciparum","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"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":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/nar/gkg627","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg627","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3843/9487660/gkg627.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:12824434","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12824434","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}],"best_oa_location":{"id":"doi:10.1093/nar/gkg627","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg627","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3843/9487660/gkg627.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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2119447107.pdf","grobid_xml":"https://content.openalex.org/works/W2119447107.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W111213550","https://openalex.org/W145348557","https://openalex.org/W176261813","https://openalex.org/W1535283155","https://openalex.org/W1587722196","https://openalex.org/W1778599501","https://openalex.org/W1976016360","https://openalex.org/W1977003396","https://openalex.org/W1985182388","https://openalex.org/W1990351127","https://openalex.org/W1996259602","https://openalex.org/W2010402743","https://openalex.org/W2012210882","https://openalex.org/W2017147864","https://openalex.org/W2019851585","https://openalex.org/W2025956225","https://openalex.org/W2027334673","https://openalex.org/W2042282283","https://openalex.org/W2077740252","https://openalex.org/W2098822637","https://openalex.org/W2118750431","https://openalex.org/W2123766602","https://openalex.org/W2126466006","https://openalex.org/W2141652419","https://openalex.org/W2168393276","https://openalex.org/W2741340870","https://openalex.org/W6600217008"],"related_works":["https://openalex.org/W2086525401","https://openalex.org/W2006735166","https://openalex.org/W2079327011","https://openalex.org/W2053325634","https://openalex.org/W3178279768","https://openalex.org/W193851735","https://openalex.org/W4379231730","https://openalex.org/W2773861473","https://openalex.org/W1971903861","https://openalex.org/W3047903919"],"abstract_inverted_index":{"The":[0],"GeneFizz":[1,77],"(http://pbga.pasteur.fr/GeneFizz)":[2],"web":[3],"tool":[4],"permits":[5],"the":[6,19,34,46,63,98,106,110],"direct":[7],"comparison":[8],"between":[9,38,62,109],"two":[10,64,75,82,111],"types":[11,65,112],"of":[12,57,66,88,100,113],"segmentations":[13],"for":[14,59,81,94],"DNA":[15],"sequences":[16],"(possibly":[17],"annotated):":[18],"coding/non-coding":[20],"segmentation":[21,37],"associated":[22],"with":[23],"genomic":[24],"annotations":[25],"(simple":[26],"genes":[27,90],"or":[28,97],"exons":[29],"in":[30],"split":[31],"genes)":[32],"and":[33,40],"physics-based":[35,86],"structural":[36],"helix":[39],"coil":[41],"domains":[42],"(as":[43,91],"provided":[44],"by":[45,105],"classical":[47],"helix-coil":[48],"model).":[49],"There":[50],"appears":[51],"to":[52,71],"be":[53,79],"a":[54],"varying":[55],"degree":[56],"coincidence":[58],"different":[60],"genomes":[61],"segmentations,":[67],"from":[68],"almost":[69],"perfect":[70],"non-relevant.":[72],"Following":[73],"these":[74],"extremes,":[76],"can":[78],"used":[80],"purposes:":[83],"ab":[84],"initio":[85],"identification":[87],"new":[89],"recently":[92],"shown":[93],"Plasmodium":[95],"falciparum)":[96],"exploration":[99],"possible":[101],"evolutionary":[102],"signals":[103],"revealed":[104],"discrepancies":[107],"observed":[108],"information.":[114]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}