{"id":"https://openalex.org/W2118286674","doi":"https://doi.org/10.1093/nar/gki356","title":"Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies","display_name":"Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies","publication_year":2005,"publication_date":"2005-06-26","ids":{"openalex":"https://openalex.org/W2118286674","doi":"https://doi.org/10.1093/nar/gki356","mag":"2118286674","pmid":"https://pubmed.ncbi.nlm.nih.gov/15980536"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki356","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki356","pdf_url":null,"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,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gki356","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024324359","display_name":"Sacha A. F. T. van Hijum","orcid":"https://orcid.org/0000-0003-0741-2991"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"S. A. F. T. van Hijum","raw_affiliation_strings":["Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, PO Box 14, 9750 AA Haren, The Netherlands","Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, PO Box 14, 9750 AA, Haren, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, PO Box 14, 9750 AA Haren, The Netherlands","institution_ids":[]},{"raw_affiliation_string":"Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, PO Box 14, 9750 AA, Haren, the Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042804725","display_name":"Aldert Zomer","orcid":"https://orcid.org/0000-0002-0758-5190"},"institutions":[{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"A. L. Zomer","raw_affiliation_strings":["Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen  PO Box 14, 9750 AA Haren, The Netherlands","Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, PO Box 14, 9750 AA, Haren, the Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen  PO Box 14, 9750 AA Haren, The Netherlands","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, PO Box 14, 9750 AA, Haren, the Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017781414","display_name":"Oscar P. Kuipers","orcid":"https://orcid.org/0000-0001-5596-7735"},"institutions":[{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"O. P. Kuipers","raw_affiliation_strings":["Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen  PO Box 14, 9750 AA Haren, The Netherlands","Molecular Genetics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen  PO Box 14, 9750 AA Haren, The Netherlands","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"Molecular Genetics","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024844426","display_name":"Jan Kok","orcid":"https://orcid.org/0000-0001-8259-1008"},"institutions":[{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"J. Kok","raw_affiliation_strings":["Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen  PO Box 14, 9750 AA Haren, The Netherlands","Molecular Genetics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen  PO Box 14, 9750 AA Haren, The Netherlands","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"Molecular Genetics","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5024324359"],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.8791,"has_fulltext":false,"cited_by_count":84,"citation_normalized_percentile":{"value":0.72120809,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"33","issue":"Web Server","first_page":"W560","last_page":"W566"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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":0.9973000288009644,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9944999814033508,"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/contig","display_name":"Contig","score":0.8926447033882141},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7650899887084961},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7235515713691711},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.598234236240387},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5637635588645935},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.42408284544944763},{"id":"https://openalex.org/keywords/hybrid-genome-assembly","display_name":"Hybrid genome assembly","score":0.4183726906776428},{"id":"https://openalex.org/keywords/primer","display_name":"Primer (cosmetics)","score":0.4123905897140503},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16357040405273438}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.8926447033882141},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7650899887084961},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7235515713691711},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.598234236240387},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5637635588645935},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.42408284544944763},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.4183726906776428},{"id":"https://openalex.org/C2777563447","wikidata":"https://www.wikidata.org/wiki/Q7243397","display_name":"Primer (cosmetics)","level":2,"score":0.4123905897140503},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16357040405273438},{"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/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"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":"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gki356","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki356","pdf_url":null,"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,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15980536","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15980536","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pure.rug.nl:openaire/3574917c-9ef2-4ddb-a5ef-5312751cebe6","is_oa":true,"landing_page_url":"https://research.rug.nl/en/publications/3574917c-9ef2-4ddb-a5ef-5312751cebe6","pdf_url":null,"source":{"id":"https://openalex.org/S4306400420","display_name":"University of Groningen research database (University of Groningen / Centre for Information Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I169381384","host_organization_name":"University of Groningen","host_organization_lineage":["https://openalex.org/I169381384"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"van Hijum, SAFT, Zomer, AL, Kuipers, OP & Kok, J 2005, 'Projector 2 : contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies', Nucleic Acids Res., vol. 33, no. Web Server issue, pp. W560-W566. https://doi.org/10.1093/nar/gki356","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:europepmc.org:155154","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1160117","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gki356","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki356","pdf_url":null,"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,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320290","display_name":"University of Oxford","ror":"https://ror.org/052gg0110"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1499500424","https://openalex.org/W1985238140","https://openalex.org/W1996332482","https://openalex.org/W2001357952","https://openalex.org/W2055043387","https://openalex.org/W2101066810","https://openalex.org/W2107282968","https://openalex.org/W2118472493","https://openalex.org/W2130320359","https://openalex.org/W2140020602","https://openalex.org/W2153232310","https://openalex.org/W2161566573","https://openalex.org/W2164217177","https://openalex.org/W2166702270","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2127651281","https://openalex.org/W3167837387","https://openalex.org/W2993223466","https://openalex.org/W2949198880","https://openalex.org/W2944010518","https://openalex.org/W2157888653","https://openalex.org/W2131813051","https://openalex.org/W2613464961","https://openalex.org/W2089480001","https://openalex.org/W4381279187"],"abstract_inverted_index":{"With":[0],"genome":[1,35,133,157,160],"sequencing":[2],"efforts":[3],"increasing":[4],"exponentially,":[5],"valuable":[6],"information":[7,32,53],"accumulates":[8],"on":[9],"genomic":[10,21],"content":[11],"of":[12,23,38,80,96,149,154],"the":[13,128,147],"various":[14],"organisms":[15],"sequenced.":[16,43],"Projector":[17,68],"2":[18,69],"uses":[19],"(un)finished":[20],"sequences":[22,123],"an":[24],"organism":[25,41],"as":[26],"a":[27,34,39,74,97,155],"template":[28,98,156],"to":[29,172],"infer":[30],"linkage":[31,52],"for":[33,49,88,101],"sequence":[36,134],"assembly":[37],"related":[40],"being":[42],"The":[44,174],"remaining":[45,129],"gaps":[46,130],"between":[47],"contigs":[48],"which":[50],"no":[51],"is":[54,136,177],"present":[55],"can":[56,105],"subsequently":[57],"be":[58,107],"closed":[59],"with":[60,65,164],"direct":[61],"PCR":[62,103],"strategies.":[63],"Compared":[64],"other":[66],"implementations,":[67],"has":[70],"several":[71],"distinctive":[72],"features:":[73],"user-friendly":[75],"web":[76,175],"interface,":[77],"automatic":[78],"removal":[79],"repetitive":[81,125],"elements":[82],"(repeat-masking)":[83],"and":[84,124,141],"automated":[85],"primer":[86],"design":[87,110],"gap-closure":[89],"purposes.":[90],"Moreover,":[91],"when":[92],"using":[93],"multiple":[94,152],"fragments":[95,153],"genome,":[99],"primers":[100],"multiplex":[102],"strategies":[104],"also":[106],"designed.":[108],"Primer":[109],"takes":[111],"into":[112],"account":[113],"that,":[114],"in":[115,131,162,167],"many":[116],"cases,":[117],"contig":[118],"ends":[119],"contain":[120],"unreliable":[121],"DNA":[122],"sequences.":[126],"Closing":[127],"prokaryotic":[132],"assemblies":[135],"thereby":[137],"made":[138],"very":[139],"efficient":[140],"virtually":[142],"effortless.":[143],"We":[144],"demonstrate":[145],"that":[146],"use":[148],"single":[150],"or":[151],"(i.e.":[158],"unfinished":[159],"sequences)":[161],"combination":[163],"repeat-masking":[165],"results":[166],"mapping":[168],"success":[169],"rates":[170],"close":[171],"100%.":[173],"interface":[176],"freely":[178],"accessible":[179],"at":[180],"http://molgen.biol.rug.nl/websoftware/projector2.":[181]},"counts_by_year":[{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":8}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
