{"id":"https://openalex.org/W2090769878","doi":"https://doi.org/10.1186/1471-2105-8-189","title":"MATLIGN: a motif clustering, comparison and matching tool","display_name":"MATLIGN: a motif clustering, comparison and matching tool","publication_year":2007,"publication_date":"2007-06-08","ids":{"openalex":"https://openalex.org/W2090769878","doi":"https://doi.org/10.1186/1471-2105-8-189","mag":"2090769878","pmid":"https://pubmed.ncbi.nlm.nih.gov/17559640"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-189","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-189","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-189","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-189","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000875080","display_name":"Matti Kankainen","orcid":"https://orcid.org/0000-0002-4714-9481"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I2800229700","display_name":"Helsinki Institute of Physics","ror":"https://ror.org/01x2x1522","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I2800229700","https://openalex.org/I63548447","https://openalex.org/I94722563","https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Matti Kankainen","raw_affiliation_strings":["Institute of Biotechnology, University of Helsinki, Helsinki, Finland. matti.kankainen@helsinki.fi","Institute of Biotechnology, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, University of Helsinki, Helsinki, Finland. matti.kankainen@helsinki.fi","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I2800229700"]},{"raw_affiliation_string":"Institute of Biotechnology, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000878403","display_name":"Ari L\u00f6ytynoja","orcid":null},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ari L\u00f6ytynoja","raw_affiliation_strings":["EMBL-European Bioinformatics Institute, Hinxton, UK","EMBL \u2013 European Bioinformatics Institute, Hinxton, UK#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EMBL-European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"EMBL \u2013 European Bioinformatics Institute, Hinxton, UK#TAB#","institution_ids":["https://openalex.org/I1303153112"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000875080"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I2800229700"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.6286,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.66870713,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"8","issue":"1","first_page":"189","last_page":"189"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.992900013923645,"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":0.992900013923645,"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":0.0012000000569969416,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.000699999975040555,"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/cluster-analysis","display_name":"Cluster analysis","score":0.6188368797302246},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.5943491458892822},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.58144211769104},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5717294812202454},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4773019552230835},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4131966531276703},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3582068085670471},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33663809299468994},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3296669125556946},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29087382555007935},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23200330138206482},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1436457633972168},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1091124415397644},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.07709410786628723},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.0758180022239685}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6188368797302246},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.5943491458892822},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.58144211769104},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5717294812202454},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4773019552230835},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4131966531276703},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3582068085670471},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33663809299468994},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3296669125556946},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29087382555007935},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23200330138206482},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1436457633972168},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1091124415397644},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.07709410786628723},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0758180022239685},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","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":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-8-189","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-189","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-189","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17559640","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17559640","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:4dbea8d5dec04de1aef9fef4fa9146d1","is_oa":false,"landing_page_url":"https://doaj.org/article/4dbea8d5dec04de1aef9fef4fa9146d1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 8, Iss 1, p 189 (2007)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1925120","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1925120","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-8-189","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-189","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-189","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2090769878.pdf","grobid_xml":"https://content.openalex.org/works/W2090769878.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1590648220","https://openalex.org/W1972857806","https://openalex.org/W1987971958","https://openalex.org/W1988393300","https://openalex.org/W1992419399","https://openalex.org/W1996423252","https://openalex.org/W2017200304","https://openalex.org/W2036131961","https://openalex.org/W2044966609","https://openalex.org/W2068110028","https://openalex.org/W2068135787","https://openalex.org/W2068448872","https://openalex.org/W2084620487","https://openalex.org/W2085380917","https://openalex.org/W2088639752","https://openalex.org/W2097396311","https://openalex.org/W2110065044","https://openalex.org/W2111473801","https://openalex.org/W2113404595","https://openalex.org/W2120900302","https://openalex.org/W2123490534","https://openalex.org/W2133147430","https://openalex.org/W2158266834","https://openalex.org/W2158962723","https://openalex.org/W2165380507","https://openalex.org/W2168157737","https://openalex.org/W2939704360"],"related_works":["https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2368037387","https://openalex.org/W190186656","https://openalex.org/W2377079823","https://openalex.org/W2902352756","https://openalex.org/W2605676258","https://openalex.org/W2599962286","https://openalex.org/W2319582300","https://openalex.org/W2890847211"],"abstract_inverted_index":{"BACKGROUND:":[0],"Sequence":[1],"motifs":[2,44,82,109,147,179,194],"representing":[3],"transcription":[4,34],"factor":[5,35],"binding":[6],"sites":[7],"(TFBS)":[8],"are":[9,24,60],"commonly":[10],"encoded":[11],"as":[12,37,39],"position":[13],"frequency":[14],"matrices":[15],"(PFM)":[16],"or":[17],"degenerate":[18],"consensus":[19],"sequences":[20,87],"(CS).":[21],"These":[22],"formats":[23],"used":[25],"to":[26,40,114,120,280],"represent":[27,41],"the":[28,42,51,54,63,98,105,108,122,144,156,163,173,187,199,213,226,232],"characterised":[29,221],"TFBS":[30],"profiles":[31],"stored":[32],"in":[33,83,89,126],"databases,":[36],"well":[38],"potential":[43,261],"predicted":[45,57,110],"using":[46,148,158,202],"computational":[47,78],"methods.":[48],"To":[49],"fill":[50],"gap":[52],"between":[53],"known":[55,281],"and":[56,72,111,129,142,154],"motifs,":[58,125,263,273],"methods":[59],"needed":[61],"for":[62,69,102,231,247],"post-processing":[64,94,123,248],"of":[65,74,80,85,107,124,146,151,165,220,234,251,260,272],"prediction":[66],"results,":[67],"i.e.":[68],"matching,":[70],"comparison":[71],"clustering":[73],"pre-selected":[75],"motifs.":[76,254],"The":[77,139,184],"identification":[79],"over-represented":[81],"sets":[84],"DNA":[86,252],"is,":[88],"particular,":[90],"a":[91,135,149,218,244,257,266,269],"task":[92],"where":[93],"can":[95,210,275],"dramatically":[96],"simplify":[97],"analysis.":[99],"Efficient":[100],"post-processing,":[101],"example,":[103],"reduces":[104],"redundancy":[106],"enables":[112],"them":[113],"be":[115,277],"annotated.":[116],"RESULTS:":[117],"In":[118],"order":[119],"facilitate":[121],"both":[127],"PFM":[128,238],"CS":[130],"formats,":[131],"we":[132],"have":[133],"developed":[134],"tool":[136,140,246],"called":[137],"Matlign.":[138],"aligns":[141,178],"evaluates":[143],"similarity":[145],"combination":[150],"scoring":[152],"functions,":[153],"visualises":[155],"results":[157],"hierarchical":[159,200],"clustering.":[160],"By":[161],"limiting":[162],"number":[164,259],"distinct":[166],"gaps":[167],"created":[168],"(though,":[169],"not":[170],"their":[171],"length),":[172],"alignment":[174],"algorithm":[175],"also":[176,229],"correctly":[177],"with":[180,192,268],"an":[181],"internal":[182],"spacer.":[183],"method":[185,227],"selects":[186],"best":[188],"non-redundant":[189,270],"motif":[190,235],"set,":[191],"repetitive":[193],"merged":[195],"together,":[196],"by":[197,237],"cutting":[198],"tree":[201],"silhouette":[203],"values.":[204],"Our":[205],"analyses":[206],"show":[207],"that":[208,225],"Matlign":[209,242,264],"reliably":[211],"discover":[212],"most":[214],"similar":[215],"analogue":[216],"from":[217,256],"collection":[219],"regulatory":[222,262,282],"elements":[223],"such":[224],"is":[228,243,286],"useful":[230],"annotation":[233],"predictions":[236],"library":[239],"searches.":[240],"CONCLUSION:":[241],"user-friendly":[245],"large":[249,258],"collections":[250],"sequence":[253],"Starting":[255],"provides":[265],"researcher":[267],"set":[271],"which":[274],"then":[276],"further":[278],"associated":[279],"elements.":[283],"A":[284],"web-server":[285],"available":[287],"at":[288],"http://ekhidna.biocenter.helsinki.fi/poxo/matlign.":[289]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}