{"id":"https://openalex.org/W2029399461","doi":"https://doi.org/10.1089/cmb.2004.11.800","title":"ThurGood: Evaluating Assembly-to-Assembly Mapping","display_name":"ThurGood: Evaluating Assembly-to-Assembly Mapping","publication_year":2004,"publication_date":"2004-10-01","ids":{"openalex":"https://openalex.org/W2029399461","doi":"https://doi.org/10.1089/cmb.2004.11.800","mag":"2029399461","pmid":"https://pubmed.ncbi.nlm.nih.gov/15700403"},"language":"en","primary_location":{"id":"doi:10.1089/cmb.2004.11.800","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2004.11.800","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443","https://openalex.org/P4310320017"],"host_organization_lineage_names":["Mary Ann Liebert, Inc.","SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043310715","display_name":"Hagit Shatkay","orcid":"https://orcid.org/0000-0001-6953-3970"},"institutions":[{"id":"https://openalex.org/I189065380","display_name":"Celanese (United States)","ror":"https://ror.org/00pex3x41","country_code":"US","type":"company","lineage":["https://openalex.org/I189065380"]},{"id":"https://openalex.org/I204722609","display_name":"Queen's University","ror":"https://ror.org/02y72wh86","country_code":"CA","type":"education","lineage":["https://openalex.org/I204722609"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Hagit Shatkay","raw_affiliation_strings":["Informatics Research Group at Celera/Applied Biosystems","School of Computing, Queen's University, Kingston, Ontario","School of Computing, Queen's University Kingston Ontario Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Research Group at Celera/Applied Biosystems","institution_ids":["https://openalex.org/I189065380"]},{"raw_affiliation_string":"School of Computing, Queen's University, Kingston, Ontario","institution_ids":["https://openalex.org/I204722609"]},{"raw_affiliation_string":"School of Computing, Queen's University Kingston Ontario Canada","institution_ids":["https://openalex.org/I204722609"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072509066","display_name":"Jason Miller","orcid":"https://orcid.org/0000-0002-6912-2925"},"institutions":[{"id":"https://openalex.org/I189065380","display_name":"Celanese (United States)","ror":"https://ror.org/00pex3x41","country_code":"US","type":"company","lineage":["https://openalex.org/I189065380"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason Miller","raw_affiliation_strings":["Informatics Research Group at Celera/Applied Biosystems"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Research Group at Celera/Applied Biosystems","institution_ids":["https://openalex.org/I189065380"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010045336","display_name":"Clark Mobarry","orcid":null},"institutions":[{"id":"https://openalex.org/I189065380","display_name":"Celanese (United States)","ror":"https://ror.org/00pex3x41","country_code":"US","type":"company","lineage":["https://openalex.org/I189065380"]},{"id":"https://openalex.org/I4210127157","display_name":"Spring Techno (Germany)","ror":"https://ror.org/03ex76y18","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210127157"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Clark Mobarry","raw_affiliation_strings":["Informatics Research Group at Celera/Applied Biosystems","White Oak Technologies, 1300 Spring St., Suite 320, Silver Spring, MD 20910"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Research Group at Celera/Applied Biosystems","institution_ids":["https://openalex.org/I189065380"]},{"raw_affiliation_string":"White Oak Technologies, 1300 Spring St., Suite 320, Silver Spring, MD 20910","institution_ids":["https://openalex.org/I4210127157"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081708720","display_name":"Michael J. Flanigan","orcid":null},"institutions":[{"id":"https://openalex.org/I189065380","display_name":"Celanese (United States)","ror":"https://ror.org/00pex3x41","country_code":"US","type":"company","lineage":["https://openalex.org/I189065380"]},{"id":"https://openalex.org/I4210134499","display_name":"LEK Consulting (United States)","ror":"https://ror.org/03mjnxj17","country_code":"US","type":"company","lineage":["https://openalex.org/I4210134499"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Flanigan","raw_affiliation_strings":["Informatics Research Group at Celera/Applied Biosystems","Steck Consulting LLC, 2121 K St., NW, Washington, DC 20037"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Research Group at Celera/Applied Biosystems","institution_ids":["https://openalex.org/I189065380"]},{"raw_affiliation_string":"Steck Consulting LLC, 2121 K St., NW, Washington, DC 20037","institution_ids":["https://openalex.org/I4210134499"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015513138","display_name":"Shibu Yooseph","orcid":"https://orcid.org/0000-0001-5581-5002"},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]},{"id":"https://openalex.org/I189065380","display_name":"Celanese (United States)","ror":"https://ror.org/00pex3x41","country_code":"US","type":"company","lineage":["https://openalex.org/I189065380"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shibu Yooseph","raw_affiliation_strings":["Informatics Research Group at Celera/Applied Biosystems","J. Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Research Group at Celera/Applied Biosystems","institution_ids":["https://openalex.org/I189065380"]},{"raw_affiliation_string":"J. Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850","institution_ids":["https://openalex.org/I1301553790"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111603387","display_name":"Granger Sutton","orcid":null},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]},{"id":"https://openalex.org/I189065380","display_name":"Celanese (United States)","ror":"https://ror.org/00pex3x41","country_code":"US","type":"company","lineage":["https://openalex.org/I189065380"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Granger Sutton","raw_affiliation_strings":["Informatics Research Group at Celera/Applied Biosystems","J. Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatics Research Group at Celera/Applied Biosystems","institution_ids":["https://openalex.org/I189065380"]},{"raw_affiliation_string":"J. Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850","institution_ids":["https://openalex.org/I1301553790"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.3395,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.55433529,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"11","issue":"5","first_page":"800","last_page":"811"},"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":0.9987000226974487,"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":0.9968000054359436,"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/focus","display_name":"Focus (optics)","score":0.7034305334091187},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.6564717888832092},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6424543857574463},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5329272150993347},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.431639164686203},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29686301946640015},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22826668620109558},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09576180577278137},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0782255232334137}],"concepts":[{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.7034305334091187},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.6564717888832092},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6424543857574463},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5329272150993347},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.431639164686203},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29686301946640015},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22826668620109558},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09576180577278137},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0782255232334137},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"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/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid 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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1089/cmb.2004.11.800","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2004.11.800","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443","https://openalex.org/P4310320017"],"host_organization_lineage_names":["Mary Ann Liebert, Inc.","SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:15700403","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15700403","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1559484989","https://openalex.org/W2000390755","https://openalex.org/W2038481484","https://openalex.org/W2055043387","https://openalex.org/W2057998009","https://openalex.org/W2074231493","https://openalex.org/W2080921667","https://openalex.org/W2086991240","https://openalex.org/W2087064593","https://openalex.org/W2087686387","https://openalex.org/W2097386339","https://openalex.org/W2110291136","https://openalex.org/W2127230663","https://openalex.org/W2137986897","https://openalex.org/W2144866873","https://openalex.org/W2151464048","https://openalex.org/W2152331922","https://openalex.org/W2155237411","https://openalex.org/W2161387979","https://openalex.org/W2165270659","https://openalex.org/W3138790538"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2766401759","https://openalex.org/W3134563641"],"abstract_inverted_index":{"The":[0],"alignment":[1,27,39],"and":[2,25,32,50],"mapping":[3],"of":[4,11,52,66],"large":[5],"genomic":[6],"sequences":[7],"is":[8],"the":[9,48,67],"focus":[10],"much":[12],"recent":[13],"research.":[14],"However,":[15],"relatively":[16],"little":[17],"has":[18],"been":[19],"done":[20],"so":[21],"far":[22],"about":[23],"testing":[24],"validating":[26],"methods.":[28],"We":[29],"introduce":[30],"criteria":[31],"new":[33],"tools":[34,42],"we":[35],"have":[36,43],"developed":[37],"for":[38,55],"evaluation.":[40],"These":[41],"already":[44],"proved":[45],"useful":[46],"in":[47],"evaluation":[49],"ranking":[51],"several":[53],"methods":[54],"assembly-to-assembly":[56],"mapping,":[57],"which":[58],"were":[59],"recently":[60],"used":[61],"to":[62,70],"map":[63],"multiple":[64],"versions":[65],"human":[68],"genome":[69],"each":[71],"other":[72],"(Istrail":[73],"et":[74],"aL,":[75],"2004).":[76]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
