{"id":"https://openalex.org/W2101926478","doi":"https://doi.org/10.1093/bioinformatics/bti050","title":"Biological sequence analysis through the one-dimensional percolation transform and its enhanced version","display_name":"Biological sequence analysis through the one-dimensional percolation transform and its enhanced version","publication_year":2004,"publication_date":"2004-10-01","ids":{"openalex":"https://openalex.org/W2101926478","doi":"https://doi.org/10.1093/bioinformatics/bti050","mag":"2101926478","pmid":"https://pubmed.ncbi.nlm.nih.gov/15458984"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti050","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti050","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005669749","display_name":"Luciano da Fontoura Costa","orcid":"https://orcid.org/0000-0001-5203-4366"},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Luciano da Fontoura Costa","raw_affiliation_strings":["Cybernetic Vision Research Group, GII-IFSC, Universidade de S\u00e3o Paulo S\u00e3o Carlos, SP, Caixa Postal 369, 13560-970, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cybernetic Vision Research Group, GII-IFSC, Universidade de S\u00e3o Paulo S\u00e3o Carlos, SP, Caixa Postal 369, 13560-970, Brazil","institution_ids":["https://openalex.org/I17974374"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5005669749"],"corresponding_institution_ids":["https://openalex.org/I17974374"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.4526,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60301952,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"21","issue":"5","first_page":"608","last_page":"616"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9702000021934509,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9702000021934509,"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":0.016100000590085983,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.0019000000320374966,"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/sequence","display_name":"Sequence (biology)","score":0.6779414415359497},{"id":"https://openalex.org/keywords/percolation","display_name":"Percolation (cognitive psychology)","score":0.6344090700149536},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5135462284088135},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4711683392524719},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.406019002199173},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3735932409763336},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.32991456985473633},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19088777899742126},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13874313235282898},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10461729764938354},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.07447734475135803},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07238456606864929}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6779414415359497},{"id":"https://openalex.org/C2780457167","wikidata":"https://www.wikidata.org/wiki/Q17156484","display_name":"Percolation (cognitive psychology)","level":2,"score":0.6344090700149536},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5135462284088135},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4711683392524719},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.406019002199173},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3735932409763336},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.32991456985473633},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19088777899742126},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13874313235282898},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10461729764938354},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.07447734475135803},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07238456606864929}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D014981","descriptor_name":"Xenopus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014981","descriptor_name":"Xenopus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014981","descriptor_name":"Xenopus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014982","descriptor_name":"Xenopus laevis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014982","descriptor_name":"Xenopus laevis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014982","descriptor_name":"Xenopus laevis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014982","descriptor_name":"Xenopus laevis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014982","descriptor_name":"Xenopus laevis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014982","descriptor_name":"Xenopus laevis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029867","descriptor_name":"Xenopus Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029867","descriptor_name":"Xenopus Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029867","descriptor_name":"Xenopus Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029867","descriptor_name":"Xenopus Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029867","descriptor_name":"Xenopus Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029867","descriptor_name":"Xenopus Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029961","descriptor_name":"Zebrafish Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti050","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti050","pdf_url":null,"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:15458984","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15458984","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":"Comparative Study"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W297806015","https://openalex.org/W1544578519","https://openalex.org/W1558680194","https://openalex.org/W1921115953","https://openalex.org/W2017821362","https://openalex.org/W2024213282","https://openalex.org/W2044274267","https://openalex.org/W2048717753","https://openalex.org/W2066335468","https://openalex.org/W2094097671","https://openalex.org/W2098475202","https://openalex.org/W2108350018","https://openalex.org/W2160838724","https://openalex.org/W2167844693","https://openalex.org/W2168029153","https://openalex.org/W2168353136","https://openalex.org/W2798681570","https://openalex.org/W3113109455"],"related_works":["https://openalex.org/W2112284452","https://openalex.org/W1615233145","https://openalex.org/W2325764612","https://openalex.org/W2366858245","https://openalex.org/W4254043756","https://openalex.org/W3014732237","https://openalex.org/W3102564941","https://openalex.org/W2107801062","https://openalex.org/W2949171345","https://openalex.org/W1966598944"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,84],"necessity":[2],"to":[3,70,94,107,118],"characterize":[4],"the":[5,23,26,30,46,54,73,87,116],"spatial":[6],"uniformity":[7],"(or":[8],"lack":[9],"of":[10,12,22,25,36,49,56,62,86],"it)":[11],"symbols":[13],"in":[14,53,125],"biological":[15],"sequences,":[16],"given":[17],"its":[18],"implications":[19],"for":[20],"identification":[21],"properties":[24],"structures":[27],"associated":[28],"with":[29,92,112],"sequences.":[31],"METHODS:":[32],"A":[33],"one-dimensional":[34],"version":[35,61],"a":[37],"recently":[38],"introduced":[39],"percolation-based":[40],"approach":[41],"is":[42,77,90],"presented,":[43],"which":[44,65],"allows":[45],"accurate":[47],"quantification":[48],"symbol":[50],"distributions":[51],"even":[52],"presence":[55],"co-existing":[57],"densities.":[58],"An":[59],"enhanced":[60],"this":[63],"methodology,":[64],"uses":[66],"an":[67],"agglomerative":[68],"process":[69],"organize":[71],"hierarchically":[72],"sequence":[74],"into":[75],"subsequences,":[76],"also":[78],"proposed":[79,88],"and":[80,96,101,105],"illustrated.":[81],"3.":[82],"RESULTS:":[83],"potential":[85],"methodology":[89],"illustrated":[91],"respect":[93],"synthetic":[95],"real":[97],"data":[98],"(1881":[99],"zebrafish":[100],"1200":[102],"Xenopus":[103],"proteins)":[104],"compared":[106],"two":[108],"alternative":[109],"multiscale":[110],"methodologies,":[111],"encouraging":[113],"results":[114],"including":[115],"possibility":[117],"identify":[119],"particularly":[120],"remarkable":[121],"amino":[122],"acid":[123],"arrangements":[124],"proteins.":[126],"4.":[127],"CONTACT:":[128],"luciano@if.sc.usp.br.":[129]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}