{"id":"https://openalex.org/W2132505033","doi":"https://doi.org/10.1093/bioinformatics/bth911","title":"Tracking repeats using significance and transitivity","display_name":"Tracking repeats using significance and transitivity","publication_year":2004,"publication_date":"2004-07-19","ids":{"openalex":"https://openalex.org/W2132505033","doi":"https://doi.org/10.1093/bioinformatics/bth911","mag":"2132505033","pmid":"https://pubmed.ncbi.nlm.nih.gov/15262814"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth911","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth911","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/suppl_1/i311/576248/bth911.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/20/suppl_1/i311/576248/bth911.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064941832","display_name":"Radek Szklarczyk","orcid":null},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Radek Szklarczyk","raw_affiliation_strings":["Centre for Integrative Bioinformatics (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands","Centre for Integrative Bioinformatics (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Integrative Bioinformatics (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]},{"raw_affiliation_string":"Centre for Integrative Bioinformatics (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands#TAB#","institution_ids":["https://openalex.org/I865915315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103164604","display_name":"Jaap Heringa","orcid":"https://orcid.org/0000-0001-8641-4930"},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jaap Heringa","raw_affiliation_strings":["Centre for Integrative Bioinformatics (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands","Centre for Integrative Bioinformatics (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Integrative Bioinformatics (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]},{"raw_affiliation_string":"Centre for Integrative Bioinformatics (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands#TAB#","institution_ids":["https://openalex.org/I865915315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5064941832"],"corresponding_institution_ids":["https://openalex.org/I865915315"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.5145,"has_fulltext":true,"cited_by_count":145,"citation_normalized_percentile":{"value":0.89269556,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"20","issue":"suppl_1","first_page":"i311","last_page":"i317"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.41920000314712524,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.41920000314712524,"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":0.3327000141143799,"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/T10949","display_name":"Genetic Neurodegenerative Diseases","score":0.027000000700354576,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/transitive-relation","display_name":"Transitive relation","score":0.8289905786514282},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5996346473693848},{"id":"https://openalex.org/keywords/tracking","display_name":"Tracking (education)","score":0.5603470802307129},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4696475863456726},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4222845435142517},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3527420163154602},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21502554416656494},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20951518416404724},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.13765877485275269},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.10151252150535583}],"concepts":[{"id":"https://openalex.org/C191399111","wikidata":"https://www.wikidata.org/wiki/Q64861","display_name":"Transitive relation","level":2,"score":0.8289905786514282},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5996346473693848},{"id":"https://openalex.org/C2775936607","wikidata":"https://www.wikidata.org/wiki/Q466845","display_name":"Tracking (education)","level":2,"score":0.5603470802307129},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4696475863456726},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4222845435142517},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3527420163154602},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21502554416656494},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20951518416404724},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.13765877485275269},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.10151252150535583},{"id":"https://openalex.org/C19417346","wikidata":"https://www.wikidata.org/wiki/Q7922","display_name":"Pedagogy","level":1,"score":0.0}],"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D020449","descriptor_name":"Repetitive Sequences, Amino Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020449","descriptor_name":"Repetitive Sequences, Amino Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020449","descriptor_name":"Repetitive Sequences, Amino Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bth911","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth911","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/suppl_1/i311/576248/bth911.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:15262814","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15262814","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:research.vu.nl:openaire_cris_publications/b1cd6e74-de79-419f-895f-071329274757","is_oa":true,"landing_page_url":"https://research.vu.nl/en/publications/b1cd6e74-de79-419f-895f-071329274757","pdf_url":"https://research.vu.nl/ws/files/2001954/169707.pdf","source":{"id":"https://openalex.org/S4306401107","display_name":"VU Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I865915315","host_organization_name":"Vrije Universiteit Amsterdam","host_organization_lineage":["https://openalex.org/I865915315"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Szklarczyk, R & Heringa, J 2004, 'Tracking repeats using significance and transitivty.', Bioinformatics, vol. 20, no. Suppl 1, pp. i311-i317. https://doi.org/10.1093/bioinformatics/bth911","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bth911","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth911","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/suppl_1/i311/576248/bth911.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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2132505033.pdf","grobid_xml":"https://content.openalex.org/works/W2132505033.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W21816278","https://openalex.org/W1500214331","https://openalex.org/W1600463518","https://openalex.org/W1659313070","https://openalex.org/W1987393189","https://openalex.org/W2008560636","https://openalex.org/W2026586467","https://openalex.org/W2032295681","https://openalex.org/W2051916497","https://openalex.org/W2054849588","https://openalex.org/W2066688961","https://openalex.org/W2072056787","https://openalex.org/W2092670169","https://openalex.org/W2094104050","https://openalex.org/W2094519647","https://openalex.org/W2143210482","https://openalex.org/W2144362290","https://openalex.org/W2148311769","https://openalex.org/W2148853951","https://openalex.org/W2152398705","https://openalex.org/W2187406058","https://openalex.org/W2312194337","https://openalex.org/W4235512468","https://openalex.org/W4246833219"],"related_works":["https://openalex.org/W4312527695","https://openalex.org/W2361167282","https://openalex.org/W1528932152","https://openalex.org/W2091342995","https://openalex.org/W2271118953","https://openalex.org/W3007067598","https://openalex.org/W2359420171","https://openalex.org/W1677394555","https://openalex.org/W2073498251","https://openalex.org/W3204019825"],"abstract_inverted_index":{"MOTIVATION:":[0],"Internal":[1],"repeats":[2,32,61,78,215],"in":[3,79,85,216],"coding":[4,19],"sequences":[5,20],"correspond":[6],"to":[7,23,27,35,90,124,158],"structural":[8,197],"and":[9,41,45,97,143,146,183,207,213],"functional":[10],"units":[11],"of":[12,16,18,31,43,58,76,99,108,110,120,150,192,221],"proteins.":[13,80],"Moreover,":[14],"duplication":[15],"fragments":[17],"is":[21,33,52,102,204,243],"known":[22],"be":[24],"a":[25,68,160,165,190,205,231],"mechanism":[26],"facilitate":[28],"evolution.":[29],"Identification":[30],"crucial":[34],"shed":[36],"light":[37],"on":[38,196],"the":[39,56,100,106,118,148,240],"function":[40],"structure":[42],"proteins,":[44],"explain":[46],"their":[47],"evolutionary":[48],"past.":[49],"The":[50,94,199,235],"task":[51],"difficult":[53],"because":[54],"during":[55],"course":[57],"evolution":[59],"many":[60],"diverged":[62],"beyond":[63],"recognition.":[64],"RESULTS:":[65],"We":[66,171],"introduce":[67],"new":[69],"method":[70,101],"TRUST,":[71],"for":[72,130,181,210],"ab":[73],"initio":[74],"determination":[75],"internal":[77],"It":[81],"provides":[82],"an":[83],"improvement":[84],"prediction":[86],"quality":[87],"as":[88],"compared":[89],"alternative":[91],"state-of-the-art":[92],"methods.":[93],"increased":[95],"sensitivity":[96],"accuracy":[98],"achieved":[103],"by":[104,176],"exploiting":[105],"concept":[107],"transitivity":[109,121],"alignments.":[111,185],"Starting":[112],"from":[113],"significant":[114],"local":[115],"suboptimal":[116],"alignments,":[117],"application":[119],"allows":[122],"us":[123,157],"(1)":[125],"identify":[126],"distant":[127],"repeat":[128,167,193,224],"homologues":[129],"which":[131],"no":[132],"alignments":[133],"were":[134],"found;":[135],"(2)":[136],"gain":[137],"confidence":[138],"about":[139],"consistently":[140],"well-aligned":[141],"regions;":[142],"(3)":[144],"recognize":[145],"reduce":[147],"contribution":[149],"non-homologous":[151],"repeats.":[152],"This":[153],"re-assessment":[154],"step":[155],"enables":[156],"derive":[159],"virtually":[161],"noise-free":[162],"profile":[163],"representing":[164],"generalized":[166],"with":[168,226,239],"high":[169],"fidelity.":[170],"also":[172],"obtained":[173],"superior":[174],"specificity":[175],"employing":[177],"rigid":[178],"statistical":[179],"testing":[180],"self-sequence":[182],"profile-sequence":[184],"Assessment":[186],"was":[187],"done":[188],"using":[189],"database":[191],"annotations":[194],"based":[195],"superpositioning.":[198],"results":[200],"show":[201],"that":[202],"TRUST":[203,236],"useful":[206],"reliable":[208],"tool":[209],"mining":[211],"tandem":[212],"non-tandem":[214],"protein":[217],"sequence":[218],"databases,":[219],"capable":[220],"predicting":[222],"multiple":[223],"types":[225],"varying":[227],"intervening":[228],"segments":[229],"within":[230],"single":[232],"sequence.":[233],"AVAILABILITY:":[234],"server":[237],"(together":[238],"source":[241],"code)":[242],"available":[244],"at":[245],"http://ibivu.cs.vu.nl/programs/trustwww":[246]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":11}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}