{"id":"https://openalex.org/W2115918447","doi":"https://doi.org/10.1186/gb-2007-8-6-r124","title":"Measuring the accuracy of genome-size multiple alignments","display_name":"Measuring the accuracy of genome-size multiple alignments","publication_year":2007,"publication_date":"2007-06-26","ids":{"openalex":"https://openalex.org/W2115918447","doi":"https://doi.org/10.1186/gb-2007-8-6-r124","mag":"2115918447","pmid":"https://pubmed.ncbi.nlm.nih.gov/17594489","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2394773"},"language":"en","primary_location":{"id":"doi:10.1186/gb-2007-8-6-r124","doi":"https://doi.org/10.1186/gb-2007-8-6-r124","is_oa":true,"landing_page_url":"https://doi.org/10.1186/gb-2007-8-6-r124","pdf_url":"https://genomebiology.biomedcentral.com/counter/pdf/10.1186/gb-2007-8-6-r124","source":{"id":"https://openalex.org/S81160022","display_name":"Genome biology","issn_l":"1465-6906","issn":["1465-6906","1465-6914","1474-7596","1474-760X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"Genome Biology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://genomebiology.biomedcentral.com/counter/pdf/10.1186/gb-2007-8-6-r124","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078204276","display_name":"Amol Prakash","orcid":"https://orcid.org/0000-0002-3997-6487","observed_orcids":["https://orcid.org/0000-0002-3997-6487"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Amol Prakash","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA. amol.prakash@thermofisher.com","Department of Computer Science and Engineering, University of Washington, Seattle, WA, 98195-2350, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA. amol.prakash@thermofisher.com","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Seattle, WA, 98195-2350, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008676408","display_name":"Martin Tompa","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin Tompa","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Washington, Seattle, WA, 98195-2350, USA","Department of Genome Sciences, University of Washington, Seattle, WA, 98195-2350, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Seattle, WA, 98195-2350, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Genome Sciences, University of Washington, Seattle, WA, 98195-2350, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5078204276"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":5490,"currency":"USD","value_usd":5490},"apc_paid":{"value":5490,"currency":"USD","value_usd":5490},"fwci":2.0744,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.87148291,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"8","issue":"6","first_page":"R124","last_page":"R124"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9854000210762024,"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":0.9854000210762024,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.008500000461935997,"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"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.0019000000320374966,"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/whole-genome-alignment","display_name":"whole-genome alignment","score":0.9139999747276306},{"id":"https://openalex.org/keywords/alignment-accuracy","display_name":"alignment accuracy","score":0.8180000185966492},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"comparative genomics","score":0.796999990940094},{"id":"https://openalex.org/keywords/misalignment-detection","display_name":"misalignment detection","score":0.621999979019165},{"id":"https://openalex.org/keywords/ucsc-genome-browser","display_name":"UCSC Genome Browser","score":0.6880000233650208},{"id":"https://openalex.org/keywords/human-chromosome-1","display_name":"chromosome 1","score":0.968999981880188}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8283289670944214},{"id":"https://openalex.org/C64015301","wikidata":"https://www.wikidata.org/wiki/Q5533480","display_name":"Genome Biology","level":5,"score":0.7274785041809082},{"id":"https://openalex.org/C47042493","wikidata":"https://www.wikidata.org/wiki/Q265799","display_name":"Human genetics","level":3,"score":0.7206181287765503},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5849786996841431},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5745593309402466},{"id":"https://openalex.org/C39238701","wikidata":"https://www.wikidata.org/wiki/Q2091816","display_name":"Computational genomics","level":5,"score":0.5520447492599487},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5305004119873047},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.42254653573036194},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4175010919570923},{"id":"https://openalex.org/C61271108","wikidata":"https://www.wikidata.org/wiki/Q3180866","display_name":"Genome size","level":4,"score":0.41322416067123413},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14290288090705872}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D002878","descriptor_name":"Chromosomes, Human, Pair 1","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":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","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":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/gb-2007-8-6-r124","doi":"https://doi.org/10.1186/gb-2007-8-6-r124","is_oa":true,"landing_page_url":"https://doi.org/10.1186/gb-2007-8-6-r124","pdf_url":"https://genomebiology.biomedcentral.com/counter/pdf/10.1186/gb-2007-8-6-r124","source":{"id":"https://openalex.org/S81160022","display_name":"Genome biology","issn_l":"1465-6906","issn":["1465-6906","1465-6914","1474-7596","1474-760X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"Genome Biology","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2394773","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2394773","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Biol","raw_type":"Text"},{"id":"pmid:17594489","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17594489","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,"listed_in":[],"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":"Genome biology","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.164.1448","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.164.1448","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.californiacityfinance.com/WC0306OriginDevolution.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.208.9834","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.208.9834","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://genomebiology.com/content/pdf/gb-2007-8-6-r124.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1186/gb-2007-8-6-r124","doi":"https://doi.org/10.1186/gb-2007-8-6-r124","is_oa":true,"landing_page_url":"https://doi.org/10.1186/gb-2007-8-6-r124","pdf_url":"https://genomebiology.biomedcentral.com/counter/pdf/10.1186/gb-2007-8-6-r124","source":{"id":"https://openalex.org/S81160022","display_name":"Genome biology","issn_l":"1465-6906","issn":["1465-6906","1465-6914","1474-7596","1474-760X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"Genome Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1836573911","display_name":"ITR: Discovering Regulatory Elements in Biological Sequences","funder_award_id":"0218798","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6592501878","display_name":"Discovering Motifs From Orthologous Sequences","funder_award_id":"R01HG002602","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G7224960661","display_name":"New Methods for High-Resolution Comparative Modeling","funder_award_id":"P20GM076222","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"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/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2115918447.pdf","grobid_xml":"https://content.openalex.org/works/W2115918447.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W11679311","https://openalex.org/W267555217","https://openalex.org/W639252573","https://openalex.org/W1509502258","https://openalex.org/W1965998064","https://openalex.org/W1974736226","https://openalex.org/W2055043387","https://openalex.org/W2068663572","https://openalex.org/W2077026347","https://openalex.org/W2085442947","https://openalex.org/W2094519647","https://openalex.org/W2100990361","https://openalex.org/W2102424972","https://openalex.org/W2112132489","https://openalex.org/W2116251070","https://openalex.org/W2128016314","https://openalex.org/W2138245520","https://openalex.org/W2158826174","https://openalex.org/W2161978970","https://openalex.org/W2167359290","https://openalex.org/W2247766769","https://openalex.org/W7033432882","https://openalex.org/W7098228260","https://openalex.org/W7099666281"],"related_works":["https://openalex.org/W2139317640","https://openalex.org/W6981019023","https://openalex.org/W7045272329","https://openalex.org/W2058494629","https://openalex.org/W7096764993","https://openalex.org/W1997631042","https://openalex.org/W2110172970","https://openalex.org/W2905220772","https://openalex.org/W2111551123","https://openalex.org/W2802024668"],"abstract_inverted_index":{"Whole-genome":[0],"alignments":[1],"are":[2],"invaluable":[3],"for":[4],"comparative":[5,10],"genomics.":[6],"Before":[7],"doing":[8],"any":[9],"analysis":[11],"on":[12],"a":[13,27],"region":[14],"of":[15,33,36,54,69],"interest,":[16],"one":[17],"must":[18],"have":[19],"confidence":[20],"in":[21],"that":[22,67],"region's":[23],"alignment.":[24,48],"We":[25,49,63],"provide":[26],"methodology":[28],"to":[29,42],"measure":[30],"the":[31,43,55],"accuracy":[32],"arbitrary":[34],"regions":[35,72],"these":[37,70],"alignments,":[38],"and":[39],"apply":[40],"it":[41],"UCSC":[44],"Genome":[45],"Browser's":[46],"17-vertebrate":[47],"identify":[50],"9.7%":[51],"(21":[52],"Mbp)":[53],"human":[56],"chromosome":[57],"1":[58],"alignment":[59],"as":[60],"suspiciously":[61],"aligned.":[62],"present":[64],"independent":[65],"evidence":[66],"many":[68],"suspicious":[71],"represent":[73],"misalignments.":[74]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}