{"id":"https://openalex.org/W4226061652","doi":"https://doi.org/10.1093/nar/gkac301","title":"Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes","display_name":"Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes","publication_year":2022,"publication_date":"2022-04-15","ids":{"openalex":"https://openalex.org/W4226061652","doi":"https://doi.org/10.1093/nar/gkac301","pmid":"https://pubmed.ncbi.nlm.nih.gov/35524553"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkac301","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac301","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/gkac301","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068396282","display_name":"Shucheng Liu","orcid":"https://orcid.org/0000-0002-1775-8470"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Shu-Cheng Liu","raw_affiliation_strings":["Department of Computer Science, National Tsing Hua University , Hsinchu 30013, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National Tsing Hua University , Hsinchu 30013, Taiwan","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015419789","display_name":"Yan-Ru Ju","orcid":null},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yan-Ru Ju","raw_affiliation_strings":["Department of Computer Science, National Tsing Hua University , Hsinchu 30013, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National Tsing Hua University , Hsinchu 30013, Taiwan","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101852068","display_name":"Chin Lung Lu","orcid":"https://orcid.org/0000-0002-4025-2558"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chin Lung Lu","raw_affiliation_strings":["Department of Computer Science, National Tsing Hua University , Hsinchu 30013, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National Tsing Hua University , Hsinchu 30013, Taiwan","institution_ids":["https://openalex.org/I25846049"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5068396282"],"corresponding_institution_ids":["https://openalex.org/I25846049"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.2148,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.77680385,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"50","issue":"W1","first_page":"W500","last_page":"W509"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T11482","display_name":"RNA modifications and cancer","score":0.9958999752998352,"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","display_name":"Genome","score":0.8188365697860718},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.7654346227645874},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.6196393966674805},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5633507370948792},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5551811456680298},{"id":"https://openalex.org/keywords/correctness","display_name":"Correctness","score":0.5134740471839905},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.485867440700531},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48418715596199036},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3997924327850342},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15158745646476746},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.10795986652374268},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.10062804818153381}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8188365697860718},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.7654346227645874},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.6196393966674805},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5633507370948792},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5551811456680298},{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.5134740471839905},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.485867440700531},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48418715596199036},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3997924327850342},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15158745646476746},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.10795986652374268},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.10062804818153381}],"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":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkac301","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac301","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:35524553","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35524553","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:pubmedcentral.nih.gov:9252826","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9252826","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkac301","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac301","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":[{"id":"https://openalex.org/G5119230040","display_name":null,"funder_award_id":"MOST110-2221-E-007-083-MY2","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"}],"funders":[{"id":"https://openalex.org/F4320322795","display_name":"Ministry of Science and Technology, Taiwan","ror":"https://ror.org/02kv4zf79"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W2020006618","https://openalex.org/W2061338306","https://openalex.org/W2096375646","https://openalex.org/W2107282968","https://openalex.org/W2113079985","https://openalex.org/W2118286674","https://openalex.org/W2122701921","https://openalex.org/W2146842681","https://openalex.org/W2155064619","https://openalex.org/W2157624015","https://openalex.org/W2158804744","https://openalex.org/W2164424155","https://openalex.org/W2165336044","https://openalex.org/W2170525352","https://openalex.org/W2215546250","https://openalex.org/W2225557190","https://openalex.org/W2564898509","https://openalex.org/W2753019977","https://openalex.org/W2799822380","https://openalex.org/W2903541438","https://openalex.org/W2907751368","https://openalex.org/W2948487375","https://openalex.org/W2952386282","https://openalex.org/W2981615389","https://openalex.org/W3096951695","https://openalex.org/W3129402903"],"related_works":["https://openalex.org/W4381279187","https://openalex.org/W2115108201","https://openalex.org/W2108742089","https://openalex.org/W4283384467","https://openalex.org/W2279684808","https://openalex.org/W3137911940","https://openalex.org/W2909852840","https://openalex.org/W3217304749","https://openalex.org/W2894932706","https://openalex.org/W2066142713"],"abstract_inverted_index":{"Multi-CSAR":[0,39,122,145,154,192],"is":[1,193],"a":[2,20,32,60,81,93,182],"web":[3],"server":[4],"that":[5],"can":[6,110],"efficiently":[7],"and":[8,12,35,49,72,99,132,167,180],"more":[9,102],"accurately":[10],"order":[11],"orient":[13],"the":[14,17,46,63,76,88,115,129,151,170,175,188],"contigs":[15,179],"in":[16,105,160,181,190],"assembly":[18],"of":[19,118,177],"target":[21,33,47,64,94],"genome":[22,34,48,65,95],"into":[23,80],"larger":[24],"scaffolds":[25,79],"based":[26,66],"on":[27,67,136,140],"multiple":[28,36,82,157],"reference":[29,37,51,70,103,119,130],"genomes.":[30],"Given":[31],"genomes,":[38],"first":[40],"identifies":[41],"sequence":[42,56,148],"markers":[43,57],"shared":[44],"between":[45],"each":[50,68],"genome,":[52,71],"then":[53],"utilizes":[54],"these":[55],"to":[58,91,96,113,123,146,172,185],"compute":[59],"scaffold":[61,159,189],"for":[62,121,128,144,169],"single":[69,77],"finally":[73],"combines":[74],"all":[75],"reference-derived":[78,83,158],"scaffold.":[84],"To":[85],"run":[86],"Multi-CSAR,":[87],"users":[89,109,171],"need":[90],"upload":[92],"be":[97],"scaffolded":[98,178],"one":[100],"or":[101,138],"genomes":[104,131],"multi-FASTA":[106],"format.":[107],"The":[108],"also":[111],"choose":[112,133],"use":[114],"'weighting":[116],"scheme":[117],"genomes'":[120],"automatically":[124],"calculate":[125],"different":[126],"weights":[127],"either":[134],"'NUCmer":[135],"nucleotides'":[137],"'PROmer":[139],"translated":[141],"amino":[142],"acids'":[143],"identify":[147],"markers.":[149],"In":[150],"output":[152],"page,":[153],"displays":[155],"its":[156],"two":[161],"graphical":[162],"representations":[163],"(i.e.":[164],"Circos":[165],"plot":[166],"dotplot)":[168],"visually":[173],"validate":[174,187],"correctness":[176],"tabular":[183],"representation":[184],"further":[186],"detail.":[191],"available":[194],"online":[195],"at":[196],"http://genome.cs.nthu.edu.tw/Multi-CSAR/.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3}],"updated_date":"2026-03-17T09:09:15.849793","created_date":"2025-10-10T00:00:00"}
