{"id":"https://openalex.org/W2148014281","doi":"https://doi.org/10.1093/bioinformatics/17.suppl_1.s207","title":"An algorithm for finding signals of unknown length in DNA sequences","display_name":"An algorithm for finding signals of unknown length in DNA sequences","publication_year":2001,"publication_date":"2001-06-01","ids":{"openalex":"https://openalex.org/W2148014281","doi":"https://doi.org/10.1093/bioinformatics/17.suppl_1.s207","mag":"2148014281","pmid":"https://pubmed.ncbi.nlm.nih.gov/11473011"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/17.suppl_1.s207","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/17.suppl_1.s207","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":true,"oa_status":"green","oa_url":"https://www.openaccessrepository.it/record/100569","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067492946","display_name":"Giulio Pavesi","orcid":"https://orcid.org/0000-0001-5705-6249"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Giulio Pavesi","raw_affiliation_strings":["Department of Computer Science, Systems and Communication, University of Milan-Bicocca, Via Bicocca degli Arcimboldi 8, Milan, I-20126, Italy. pavesi@disco.unimib.it","Department of Computer Science, Systems and Communication, University of Milan-Bicocca, Via Bicocca degli Arcimboldi 8, Milan, I-20126, Italy and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Systems and Communication, University of Milan-Bicocca, Via Bicocca degli Arcimboldi 8, Milan, I-20126, Italy. pavesi@disco.unimib.it","institution_ids":["https://openalex.org/I66752286"]},{"raw_affiliation_string":"Department of Computer Science, Systems and Communication, University of Milan-Bicocca, Via Bicocca degli Arcimboldi 8, Milan, I-20126, Italy and","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073163964","display_name":"Giancarlo Mauri","orcid":"https://orcid.org/0000-0003-3520-4022"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giancarlo Mauri","raw_affiliation_strings":["Department of Computer Science, Systems and Communication, University of Milan-Bicocca, Via Bicocca degli Arcimboldi 8, Milan, I-20126, Italy and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Systems and Communication, University of Milan-Bicocca, Via Bicocca degli Arcimboldi 8, Milan, I-20126, Italy and","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005312066","display_name":"Graziano Pesole","orcid":"https://orcid.org/0000-0003-3663-0859"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Graziano Pesole","raw_affiliation_strings":["Department of General Physiology and Biochemistry, University of Milan, Via Celoria 20, Milan, I-20133, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of General Physiology and Biochemistry, University of Milan, Via Celoria 20, Milan, I-20133, Italy","institution_ids":["https://openalex.org/I189158943"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5067492946"],"corresponding_institution_ids":["https://openalex.org/I66752286"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":11.6882,"has_fulltext":false,"cited_by_count":342,"citation_normalized_percentile":{"value":0.98376357,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"17","issue":"suppl_1","first_page":"S207","last_page":"S214"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980999827384949,"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/algorithm","display_name":"Algorithm","score":0.7342870235443115},{"id":"https://openalex.org/keywords/enumeration","display_name":"Enumeration","score":0.6858781576156616},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6577138304710388},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.5504506826400757},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5343500971794128},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.47148463129997253},{"id":"https://openalex.org/keywords/sort","display_name":"sort","score":0.46136918663978577},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4498233199119568},{"id":"https://openalex.org/keywords/position","display_name":"Position (finance)","score":0.41266492009162903},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.31870919466018677},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17948505282402039},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.16231414675712585},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15781211853027344}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.7342870235443115},{"id":"https://openalex.org/C156340839","wikidata":"https://www.wikidata.org/wiki/Q2704791","display_name":"Enumeration","level":2,"score":0.6858781576156616},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6577138304710388},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.5504506826400757},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5343500971794128},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.47148463129997253},{"id":"https://openalex.org/C88548561","wikidata":"https://www.wikidata.org/wiki/Q347599","display_name":"sort","level":2,"score":0.46136918663978577},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4498233199119568},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.41266492009162903},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.31870919466018677},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17948505282402039},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.16231414675712585},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15781211853027344},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D005821","descriptor_name":"Genetic Techniques","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D005821","descriptor_name":"Genetic Techniques","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D005821","descriptor_name":"Genetic Techniques","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/17.suppl_1.s207","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/17.suppl_1.s207","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:11473011","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11473011","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:boa.unimib.it:10281/2559","is_oa":false,"landing_page_url":"http://hdl.handle.net/10281/2559","pdf_url":null,"source":{"id":"https://openalex.org/S4306401259","display_name":"BOA (University of Milano-Bicocca)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:zenodo.org:100569","is_oa":true,"landing_page_url":"https://www.openaccessrepository.it/record/100569","pdf_url":null,"source":{"id":"https://openalex.org/S4306402478","display_name":"INFM-OAR (INFN Catania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210116497","host_organization_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Catania","host_organization_lineage":["https://openalex.org/I4210116497"],"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":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:100569","is_oa":true,"landing_page_url":"https://www.openaccessrepository.it/record/100569","pdf_url":null,"source":{"id":"https://openalex.org/S4306402478","display_name":"INFM-OAR (INFN Catania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210116497","host_organization_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Catania","host_organization_lineage":["https://openalex.org/I4210116497"],"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":"","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1486659038","https://openalex.org/W1580213736","https://openalex.org/W1983921490","https://openalex.org/W1990061958","https://openalex.org/W1998300401","https://openalex.org/W2003967338","https://openalex.org/W2014459399","https://openalex.org/W2028904582","https://openalex.org/W2035588418","https://openalex.org/W2054984882","https://openalex.org/W2056002855","https://openalex.org/W2059513841","https://openalex.org/W2085239230","https://openalex.org/W2115772919","https://openalex.org/W2121252285","https://openalex.org/W2152893838","https://openalex.org/W2155976638","https://openalex.org/W2159588654","https://openalex.org/W2162600254","https://openalex.org/W2166086559","https://openalex.org/W2320748401","https://openalex.org/W2533248932"],"related_works":["https://openalex.org/W108845024","https://openalex.org/W2406961474","https://openalex.org/W4300125793","https://openalex.org/W2578985712","https://openalex.org/W2952598754","https://openalex.org/W3042106073","https://openalex.org/W2143566611","https://openalex.org/W4251460363","https://openalex.org/W588267724","https://openalex.org/W2057205169"],"abstract_inverted_index":{"Pattern":[0],"discovery":[1],"in":[2,10,28,34,72,80,102,150],"unaligned":[3],"DNA":[4,35],"sequences":[5,36,89,106],"is":[6,117,126,183],"a":[7,55,86,138,142,195],"challenging":[8],"problem":[9,49],"both":[11],"computer":[12],"science":[13],"and":[14,20,40,90,155,205],"molecular":[15],"biology.":[16],"Several":[17],"different":[18],"methods":[19,45],"techniques":[21],"have":[22,187],"been":[23],"proposed":[24],"so":[25,156],"far,":[26],"but":[27],"most":[29,112,147],"of":[30,58,77,88,107,120,131,141,177,190,193],"the":[31,48,74,108,118,121,129,134,151,162,175,191,199,202,206,221,225],"cases":[32],"signals":[33,53],"are":[37],"very":[38],"complicated":[39],"avoid":[41],"detection.":[42],"Exact":[43],"exhaustive":[44,65],"can":[46,144,164,171,216],"solve":[47],"only":[50,124],"for":[51],"short":[52],"with":[54,110],"limited":[56],"number":[57],"mutations.":[59,178],"In":[60,179],"this":[61,81,180],"work,":[62],"we":[63,159,210],"extend":[64],"enumeration":[66],"also":[67,167,184],"to":[68,186,198,219],"longer":[69],"patterns.":[70],"More":[71],"detail,":[73],"basic":[75],"version":[76],"algorithm":[78,163],"presented":[79],"paper,":[82],"given":[83],"as":[84],"input":[85,207],"set":[87,109],"an":[91,188],"error":[92,203],"ratio":[93],"epsilon":[94],"<":[95],"1,":[96],"finds":[97],"all":[98],"patterns":[99,222],"that":[100,215],"occur":[101],"at":[103,111,146],"least":[104],"q":[105],"epsilonm":[113],"mutations,":[114],"where":[115],"m":[116],"length":[119],"pattern.":[122],"The":[123],"restriction":[125],"imposed":[127],"on":[128,174],"location":[130],"mutations":[132],"along":[133],"signal.":[135],"That":[136],"is,":[137],"valid":[139],"occurrence":[140],"pattern":[143],"present":[145],"[epsiloni]":[148],"mismatches":[149],"first":[152],"i":[153],"nucleotides,":[154],"on.":[157],"However,":[158],"show":[160],"how":[161],"be":[165,172,217],"used":[166,218],"when":[168],"no":[169],"assumption":[170],"made":[173],"position":[176],"case,":[181],"it":[182],"possible":[185],"estimate":[189],"probability":[192],"finding":[194],"signal":[196,200],"according":[197],"length,":[201],"ratio,":[204],"parameters.":[208],"Finally,":[209],"discuss":[211],"some":[212],"significance":[213],"measures":[214],"sort":[220],"output":[223],"by":[224],"algorithm.":[226]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":13},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":15},{"year":2014,"cited_by_count":21},{"year":2013,"cited_by_count":27},{"year":2012,"cited_by_count":30}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}