{"id":"https://openalex.org/W2105423910","doi":"https://doi.org/10.1186/1471-2105-9-15","title":"Multiple organism algorithm for finding ultraconserved elements","display_name":"Multiple organism algorithm for finding ultraconserved elements","publication_year":2008,"publication_date":"2008-01-11","ids":{"openalex":"https://openalex.org/W2105423910","doi":"https://doi.org/10.1186/1471-2105-9-15","mag":"2105423910","pmid":"https://pubmed.ncbi.nlm.nih.gov/18186941"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-15","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-15","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/10.1186/1471-2105-9-15","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078078996","display_name":"Scott Christley","orcid":"https://orcid.org/0000-0002-9889-1221"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Scott Christley","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA. schristl@nd.edu","Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA. schristl@nd.edu","institution_ids":["https://openalex.org/I107639228"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107834683","display_name":"Neil F. Lobo","orcid":null},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Neil F Lobo","raw_affiliation_strings":["Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113594168","display_name":"Greg Madey","orcid":null},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Greg Madey","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA","Interdisciplinary Center for the Study of Biocomplexity, University of Notre Dame, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA","institution_ids":["https://openalex.org/I107639228"]},{"raw_affiliation_string":"Interdisciplinary Center for the Study of Biocomplexity, University of Notre Dame, USA","institution_ids":["https://openalex.org/I107639228"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5078078996"],"corresponding_institution_ids":["https://openalex.org/I107639228"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6915,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.7030936,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"9","issue":"1","first_page":"15","last_page":"15"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9993000030517578,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.74805748462677},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.5781179070472717},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5254582166671753},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49738290905952454},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4724103510379791},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.47095948457717896},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4682264029979706},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4297296702861786},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32328373193740845},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2790960967540741},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23357930779457092}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.74805748462677},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.5781179070472717},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5254582166671753},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49738290905952454},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4724103510379791},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.47095948457717896},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4682264029979706},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4297296702861786},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32328373193740845},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2790960967540741},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23357930779457092},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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":"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":"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","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}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-9-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-15","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-15","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:18186941","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18186941","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:527c001669af45b5a0a819fe7796d4d6","is_oa":true,"landing_page_url":"https://doaj.org/article/527c001669af45b5a0a819fe7796d4d6","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 15 (2008)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1833051","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2244594","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-15","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-15","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-15","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":[{"id":"https://openalex.org/G1305528480","display_name":null,"funder_award_id":"NIH/NIAID","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5903061775","display_name":null,"funder_award_id":"NIAID","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7199261362","display_name":null,"funder_award_id":"HHSN266200400039C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2105423910.pdf","grobid_xml":"https://content.openalex.org/works/W2105423910.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W8187158","https://openalex.org/W938539187","https://openalex.org/W1531954825","https://openalex.org/W1990061958","https://openalex.org/W2057998009","https://openalex.org/W2087721273","https://openalex.org/W2090415636","https://openalex.org/W2095685450","https://openalex.org/W2095824228","https://openalex.org/W2098001104","https://openalex.org/W2100775895","https://openalex.org/W2100990361","https://openalex.org/W2107282968","https://openalex.org/W2112555386","https://openalex.org/W2116251070","https://openalex.org/W2117936709","https://openalex.org/W2124281279","https://openalex.org/W2124348703","https://openalex.org/W2127230663","https://openalex.org/W2128591967","https://openalex.org/W2134283755","https://openalex.org/W2136145671","https://openalex.org/W2143286856","https://openalex.org/W2145191876","https://openalex.org/W2147499400","https://openalex.org/W2152331922","https://openalex.org/W2155237411","https://openalex.org/W2157338021","https://openalex.org/W2158714788","https://openalex.org/W2158874082","https://openalex.org/W4210241463","https://openalex.org/W4238545668","https://openalex.org/W6806866965"],"related_works":["https://openalex.org/W24843447","https://openalex.org/W94193318","https://openalex.org/W1547180633","https://openalex.org/W2073808674","https://openalex.org/W2173289516","https://openalex.org/W322176015","https://openalex.org/W20947408","https://openalex.org/W2028140658","https://openalex.org/W2073011570","https://openalex.org/W2468061618"],"abstract_inverted_index":{"Whole":[0],"genome":[1],"comparative":[2],"analysis":[3,29],"for":[4,15,60],"multiple":[5,31],"organisms":[6],"is":[7],"both":[8],"feasible":[9],"and":[10,39,69],"desirable":[11],"in":[12,36],"our":[13],"search":[14],"biological":[16],"knowledge.":[17],"We":[18],"argue":[19],"that":[20],"bioinformatic":[21],"programs":[22],"should":[23],"be":[24],"forward":[25],"thinking":[26],"by":[27],"assuming":[28],"on":[30],"(and":[32],"possibly":[33],"large)":[34],"genomes":[35],"the":[37,71],"design":[38,49],"implementation":[40],"of":[41,53],"algorithms.":[42],"Our":[43],"algorithm":[44],"shows":[45],"how":[46],"a":[47,51],"compromise":[48],"with":[50,78],"trade-off":[52],"disk":[54],"space":[55,58],"versus":[56],"memory":[57],"allows":[59],"efficient":[61],"computation":[62],"while":[63],"only":[64],"requiring":[65],"modest":[66],"computer":[67],"resources,":[68],"at":[70],"same":[72],"time":[73],"providing":[74],"benefits":[75],"not":[76],"available":[77],"other":[79],"software.":[80]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
