{"id":"https://openalex.org/W2103052607","doi":"https://doi.org/10.1093/nar/gkj419","title":"Application of a superword array in genome assembly","display_name":"Application of a superword array in genome assembly","publication_year":2006,"publication_date":"2006-01-08","ids":{"openalex":"https://openalex.org/W2103052607","doi":"https://doi.org/10.1093/nar/gkj419","mag":"2103052607","pmid":"https://pubmed.ncbi.nlm.nih.gov/16397298","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/1325203"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj419","doi":"https://doi.org/10.1093/nar/gkj419","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj419","pdf_url":"https://academic.oup.com/nar/article-pdf/34/1/201/7128488/gkj419.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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/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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","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://academic.oup.com/nar/article-pdf/34/1/201/7128488/gkj419.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022987905","display_name":"Xiaoqiu Huang","orcid":"https://orcid.org/0000-0002-5692-6895","observed_orcids":["https://orcid.org/0000-0002-5692-6895"]},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"X. Huang","raw_affiliation_strings":["Department of Computer Science, Iowa State University, Ames, IA 50011-1040, USA. xqhuang@cs.iastate.edu","Department of Computer Science, Iowa State University, Ames, IA                         50011-1040, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Iowa State University, Ames, IA 50011-1040, USA. xqhuang@cs.iastate.edu","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Department of Computer Science, Iowa State University, Ames, IA                         50011-1040, USA","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5022987905"],"corresponding_institution_ids":["https://openalex.org/I173911158"],"apc_list":{"value":3992,"currency":"USD","value_usd":3992},"apc_paid":{"value":3992,"currency":"USD","value_usd":3992},"fwci":3.5582,"has_fulltext":true,"cited_by_count":29,"citation_normalized_percentile":{"value":0.93384615,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"34","issue":"1","first_page":"201","last_page":"205"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.8564000129699707,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.8564000129699707,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.13850000500679016,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.0012000000569969416,"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/genome-assembly","display_name":"genome assembly","score":0.9869999885559082},{"id":"https://openalex.org/keywords/sequence-matching","display_name":"sequence matching","score":0.7680000066757202},{"id":"https://openalex.org/keywords/suffix-arrays","display_name":"suffix arrays","score":0.6399999856948853},{"id":"https://openalex.org/keywords/lookup-tables","display_name":"look-up table","score":0.9380000233650208},{"id":"https://openalex.org/keywords/pcap","display_name":"PCAP","score":0.5080000162124634},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"whole genome sequencing","score":0.6010000109672546}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7324391603469849},{"id":"https://openalex.org/C2779259728","wikidata":"https://www.wikidata.org/wiki/Q281472","display_name":"Suffix array","level":3,"score":0.7281363010406494},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6221031546592712},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.5611675977706909},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.48109954595565796},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.41362079977989197},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3708729147911072},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3705105185508728},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31778159737586975},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2751046419143677},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.23741498589515686},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.18332615494728088},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06192997097969055},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006658","descriptor_name":"Histoplasma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":10,"locations":[{"id":"doi:10.1093/nar/gkj419","doi":"https://doi.org/10.1093/nar/gkj419","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj419","pdf_url":"https://academic.oup.com/nar/article-pdf/34/1/201/7128488/gkj419.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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/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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1325203","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1325203","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmid:16397298","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16397298","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":"Nucleic acids research","raw_type":"Evaluation Study"},{"id":"pmh:oai:digitalcommons.wustl.edu:open_access_pubs-1105","doi":null,"is_oa":true,"landing_page_url":"https://digitalcommons.wustl.edu/open_access_pubs/106","pdf_url":"https://digitalcommons.wustl.edu/open_access_pubs/106","source":{"id":"https://openalex.org/S4306400764","display_name":"Digital Commons@Becker (Washington University School of Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I204465549","host_organization_name":"Washington University in St. Louis","host_organization_lineage":["https://openalex.org/I204465549"],"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":"Open Access Publications","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.118.9582","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.118.9582","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://seq.cs.iastate.edu/pub/papers/201.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.548.4427","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.548.4427","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/34/1/201.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.558.8728","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.558.8728","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/34/1/201.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.771.9009","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.771.9009","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/87/5f/gkj419.PMC1325203.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.952.7204","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.952.7204","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://digitalcommons.wustl.edu/cgi/viewcontent.cgi?article%3D1105%26context%3Dopen_access_pubs","raw_type":"text"},{"id":"pmh:oai:lib.dr.iastate.edu:cs_pubs-1029","doi":null,"is_oa":true,"landing_page_url":"https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1029&context=cs_pubs","pdf_url":null,"source":{"id":"https://openalex.org/S4377196104","display_name":"Iowa State University Digital Repository (Iowa State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I173911158","host_organization_name":"Iowa State University","host_organization_lineage":["https://openalex.org/I173911158"],"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":"Computer Science Publications","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkj419","doi":"https://doi.org/10.1093/nar/gkj419","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj419","pdf_url":"https://academic.oup.com/nar/article-pdf/34/1/201/7128488/gkj419.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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/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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2899999197","display_name":"A Platform for Large-Scale Genomic Discovery","funder_award_id":"U54HG003079","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320311090","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78"},{"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"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2103052607.pdf","grobid_xml":"https://content.openalex.org/works/W2103052607.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1529802779","https://openalex.org/W1635391495","https://openalex.org/W1965331871","https://openalex.org/W1984021931","https://openalex.org/W1990061958","https://openalex.org/W2011820950","https://openalex.org/W2015292449","https://openalex.org/W2055043387","https://openalex.org/W2104189907","https://openalex.org/W2107282968","https://openalex.org/W2109062349","https://openalex.org/W2109656602","https://openalex.org/W2110291136","https://openalex.org/W2124281279","https://openalex.org/W2128591967","https://openalex.org/W2129873761","https://openalex.org/W2134283755","https://openalex.org/W2136145671","https://openalex.org/W2142619120","https://openalex.org/W2144662851","https://openalex.org/W2153889777","https://openalex.org/W2155237411","https://openalex.org/W2158874082","https://openalex.org/W2161668137","https://openalex.org/W2546836732","https://openalex.org/W2922663987","https://openalex.org/W4231413018","https://openalex.org/W7096328935","https://openalex.org/W7097764011","https://openalex.org/W7098817570"],"related_works":["https://openalex.org/W6903818781","https://openalex.org/W4382406780","https://openalex.org/W2552544363","https://openalex.org/W4228997993","https://openalex.org/W7097791268","https://openalex.org/W2155712618","https://openalex.org/W4392488280","https://openalex.org/W7063964421","https://openalex.org/W3025999138","https://openalex.org/W2968482172"],"abstract_inverted_index":{"We":[0,30],"introduce":[1],"a":[2,6,38,48,56,76,83],"data":[3],"structure":[4],"called":[5,60],"superword":[7,17,39],"array":[8,18,40],"for":[9,34,62],"finding":[10],"quickly":[11],"matches":[12],"between":[13,66],"DNA":[14],"sequences.":[15],"The":[16,51],"possesses":[19],"some":[20],"desirable":[21],"features":[22],"of":[23,44,64],"the":[24],"lookup":[25],"table":[26],"and":[27,36,73,86],"suffix":[28],"array.":[29],"describe":[31],"simple":[32],"algorithms":[33,52],"constructing":[35],"using":[37],"to":[41],"find":[42],"pairs":[43],"sequences":[45],"that":[46,80],"share":[47],"unique":[49],"superword.":[50],"are":[53],"implemented":[54],"in":[55],"genome":[57],"assembly":[58,88],"program":[59],"PCAP.REP":[61,72,81],"computation":[63],"overlaps":[65],"reads.":[67],"Experimental":[68],"results":[69],"produced":[70,82],"by":[71],"PCAP":[74],"on":[75],"whole-genome":[77],"dataset":[78],"show":[79],"more":[84],"accurate":[85],"contiguous":[87],"than":[89],"PCAP.":[90]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2012,"cited_by_count":1}],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2016-06-24T00:00:00"}