{"id":"https://openalex.org/W2114139363","doi":"https://doi.org/10.1109/bibe.2004.1317369","title":"Estimating seed sensitivity on homogeneous alignments","display_name":"Estimating seed sensitivity on homogeneous alignments","publication_year":2004,"publication_date":"2004-11-30","ids":{"openalex":"https://openalex.org/W2114139363","doi":"https://doi.org/10.1109/bibe.2004.1317369","mag":"2114139363"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2004.1317369","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2004.1317369","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/cs/0603106","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012626407","display_name":"Gr\u00e9gory Kucherov","orcid":"https://orcid.org/0000-0001-5899-5424"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I4210121838","display_name":"Laboratoire Lorrain de Recherche en Informatique et ses Applications","ror":"https://ror.org/02vnf0c38","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I277688954","https://openalex.org/I4210107720","https://openalex.org/I4210121838","https://openalex.org/I4210159245","https://openalex.org/I90183372"]},{"id":"https://openalex.org/I4210127166","display_name":"Centre Inria de l'Universit\u00e9 de Lorraine","ror":"https://ror.org/03fcjvn64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210127166"]},{"id":"https://openalex.org/I90183372","display_name":"Universit\u00e9 de Lorraine","ror":"https://ror.org/04vfs2w97","country_code":"FR","type":"education","lineage":["https://openalex.org/I90183372"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"G. Kucherov","raw_affiliation_strings":["LORIA INRIA-Lorraine, Vandoeuvre-les-Nancy, France","LORIA/INRIA-Lorraine, Villers-l\u00e8s-Nancy, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LORIA INRIA-Lorraine, Vandoeuvre-les-Nancy, France","institution_ids":["https://openalex.org/I4210121838","https://openalex.org/I1326498283","https://openalex.org/I90183372"]},{"raw_affiliation_string":"LORIA/INRIA-Lorraine, Villers-l\u00e8s-Nancy, France","institution_ids":["https://openalex.org/I4210127166","https://openalex.org/I1326498283","https://openalex.org/I4210121838"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055679303","display_name":"Laurent No\u00e9","orcid":"https://orcid.org/0000-0002-1170-8376"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I4210121838","display_name":"Laboratoire Lorrain de Recherche en Informatique et ses Applications","ror":"https://ror.org/02vnf0c38","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I277688954","https://openalex.org/I4210107720","https://openalex.org/I4210121838","https://openalex.org/I4210159245","https://openalex.org/I90183372"]},{"id":"https://openalex.org/I4210127166","display_name":"Centre Inria de l'Universit\u00e9 de Lorraine","ror":"https://ror.org/03fcjvn64","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210127166"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"L. Noe","raw_affiliation_strings":["LORIA/INRIA-Lorraine, Villers-l\u00e8s-Nancy, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LORIA/INRIA-Lorraine, Villers-l\u00e8s-Nancy, France","institution_ids":["https://openalex.org/I4210127166","https://openalex.org/I1326498283","https://openalex.org/I4210121838"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076325273","display_name":"Yann Ponty","orcid":"https://orcid.org/0000-0002-7615-3930"},"institutions":[{"id":"https://openalex.org/I102197404","display_name":"Universit\u00e9 Paris-Sud","ror":"https://ror.org/028rypz17","country_code":"FR","type":"education","lineage":["https://openalex.org/I102197404"]},{"id":"https://openalex.org/I4210144804","display_name":"Laboratoire de Recherche en Informatique","ror":"https://ror.org/04e3ktk27","country_code":"FR","type":"facility","lineage":["https://openalex.org/I102197404","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210144804","https://openalex.org/I4210159245"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Y. Ponty","raw_affiliation_strings":["LRI, Universit\u00e9 Paris-Sud, Orsay, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LRI, Universit\u00e9 Paris-Sud, Orsay, France","institution_ids":["https://openalex.org/I102197404","https://openalex.org/I4210144804"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.653,"has_fulltext":false,"cited_by_count":30,"citation_normalized_percentile":{"value":0.89897738,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"rr 4852","issue":null,"first_page":"387","last_page":"394"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"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":0.9811999797821045,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9735999703407288,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/sensitivity","display_name":"Sensitivity (control systems)","score":0.7811535596847534},{"id":"https://openalex.org/keywords/homogeneous","display_name":"Homogeneous","score":0.6577246189117432},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6207010746002197},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5689482092857361},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5645470023155212},{"id":"https://openalex.org/keywords/contrast","display_name":"Contrast (vision)","score":0.548701822757721},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5442048907279968},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.46773940324783325},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.459244042634964},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.436271607875824},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.36432820558547974},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36368703842163086},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2652934193611145},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.07531782984733582}],"concepts":[{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.7811535596847534},{"id":"https://openalex.org/C66882249","wikidata":"https://www.wikidata.org/wiki/Q169336","display_name":"Homogeneous","level":2,"score":0.6577246189117432},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6207010746002197},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5689482092857361},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5645470023155212},{"id":"https://openalex.org/C2776502983","wikidata":"https://www.wikidata.org/wiki/Q690182","display_name":"Contrast (vision)","level":2,"score":0.548701822757721},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5442048907279968},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.46773940324783325},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.459244042634964},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.436271607875824},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36432820558547974},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36368703842163086},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2652934193611145},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.07531782984733582},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":10,"locations":[{"id":"doi:10.1109/bibe.2004.1317369","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2004.1317369","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:cs/0603106","is_oa":true,"landing_page_url":"http://arxiv.org/abs/cs/0603106","pdf_url":"https://arxiv.org/pdf/cs/0603106","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.208.9666","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.208.9666","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://hal.inria.fr/docs/00/06/35/78/PDF/paper.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.341.7871","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.341.7871","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://arxiv.org/pdf/cs/0603106v1.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.504.742","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.504.742","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://hal.archives-ouvertes.fr/docs/00/06/35/78/PDF/paper.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.60.5346","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.60.5346","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.lifl.fr/~noe/./files/pp_BIBE04.ps.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.695.1316","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.695.1316","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://hal.inria.fr/inria-00001163/document/","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.75.8378","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.75.8378","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.lifl.fr/~noe/files/pp_BIBE04.pdf","raw_type":"text"},{"id":"pmh:oai:HAL:inria-00001163v1","is_oa":true,"landing_page_url":"https://inria.hal.science/inria-00001163","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1317369","raw_type":"Conference papers"},{"id":"pmh:oai:HAL:inria-00071536v1","is_oa":true,"landing_page_url":"https://inria.hal.science/inria-00071536","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"[Research Report] RR-5047, INRIA. 2003, pp.17","raw_type":"Reports"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:cs/0603106","is_oa":true,"landing_page_url":"http://arxiv.org/abs/cs/0603106","pdf_url":"https://arxiv.org/pdf/cs/0603106","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1509502258","https://openalex.org/W1528606113","https://openalex.org/W1807142859","https://openalex.org/W1873119440","https://openalex.org/W1965998064","https://openalex.org/W1972051891","https://openalex.org/W1996684294","https://openalex.org/W1998798613","https://openalex.org/W2001960495","https://openalex.org/W2015292449","https://openalex.org/W2024811036","https://openalex.org/W2052890777","https://openalex.org/W2055043387","https://openalex.org/W2055050002","https://openalex.org/W2057998009","https://openalex.org/W2087064593","https://openalex.org/W2101664494","https://openalex.org/W2109034006","https://openalex.org/W2109692166","https://openalex.org/W2112664161","https://openalex.org/W2128591967","https://openalex.org/W2129782019","https://openalex.org/W2131702282","https://openalex.org/W2136145671","https://openalex.org/W2158714788","https://openalex.org/W2160802334","https://openalex.org/W2175671778","https://openalex.org/W4236236547","https://openalex.org/W4241007652","https://openalex.org/W4293196852","https://openalex.org/W6628896446","https://openalex.org/W6630488892","https://openalex.org/W6631721822","https://openalex.org/W6643069710","https://openalex.org/W6683766045"],"related_works":["https://openalex.org/W2069592018","https://openalex.org/W2075740387","https://openalex.org/W2358990940","https://openalex.org/W2093931120","https://openalex.org/W2329812990","https://openalex.org/W1598955744","https://openalex.org/W2349116365","https://openalex.org/W3021708704","https://openalex.org/W1660242800","https://openalex.org/W2004231473"],"abstract_inverted_index":{"We":[0,29,57],"address":[1],"the":[2,6,23,48,67],"problem":[3],"of":[4,8,38,47,54],"estimating":[5],"sensitivity":[7,49],"seed-based":[9],"similarity":[10],"search":[11],"algorithms.":[12],"In":[13],"contrast":[14],"to":[15],"approaches":[16],"based":[17,25],"on":[18,26],"Markov":[19],"models,":[20],"we":[21],"study":[22],"estimation":[24],"homogeneous":[27],"alignments.":[28],"describe":[30],"an":[31,42],"algorithm":[32,43],"for":[33,44,50],"counting":[34],"and":[35,41],"random":[36],"generation":[37],"those":[39],"alignments":[40],"exact":[45],"computation":[46],"a":[51,62],"broad":[52],"class":[53],"seed":[55],"strategies.":[56],"provide":[58],"experimental":[59],"results":[60],"demonstrating":[61],"bias":[63],"introduced":[64],"by":[65],"ignoring":[66],"homogeneousness":[68],"condition.":[69]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
