{"id":"https://openalex.org/W2766330607","doi":"https://doi.org/10.1093/bioinformatics/btx713","title":"DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication","display_name":"DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication","publication_year":2017,"publication_date":"2017-11-01","ids":{"openalex":"https://openalex.org/W2766330607","doi":"https://doi.org/10.1093/bioinformatics/btx713","mag":"2766330607","pmid":"https://pubmed.ncbi.nlm.nih.gov/29106469"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx713","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx713","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btx713","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077903703","display_name":"Yasuhiro Tanizawa","orcid":"https://orcid.org/0000-0002-6294-3309"},"institutions":[{"id":"https://openalex.org/I113198587","display_name":"National Institute of Genetics","ror":"https://ror.org/02xg1m795","country_code":"JP","type":"facility","lineage":["https://openalex.org/I113198587","https://openalex.org/I1319490839","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasuhiro Tanizawa","raw_affiliation_strings":["Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan","institution_ids":["https://openalex.org/I113198587","https://openalex.org/I4210158934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046392454","display_name":"Takatomo Fujisawa","orcid":"https://orcid.org/0000-0001-8978-3344"},"institutions":[{"id":"https://openalex.org/I113198587","display_name":"National Institute of Genetics","ror":"https://ror.org/02xg1m795","country_code":"JP","type":"facility","lineage":["https://openalex.org/I113198587","https://openalex.org/I1319490839","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takatomo Fujisawa","raw_affiliation_strings":["Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan","institution_ids":["https://openalex.org/I113198587","https://openalex.org/I4210158934"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083746382","display_name":"Yasukazu Nakamura","orcid":"https://orcid.org/0000-0002-6782-5715"},"institutions":[{"id":"https://openalex.org/I113198587","display_name":"National Institute of Genetics","ror":"https://ror.org/02xg1m795","country_code":"JP","type":"facility","lineage":["https://openalex.org/I113198587","https://openalex.org/I1319490839","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I4210158934","display_name":"Research Organization of Information and Systems","ror":"https://ror.org/04p4e8t29","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yasukazu Nakamura","raw_affiliation_strings":["Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Japan","institution_ids":["https://openalex.org/I113198587","https://openalex.org/I4210158934"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5083746382"],"corresponding_institution_ids":["https://openalex.org/I113198587","https://openalex.org/I4210158934"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":24.6225,"has_fulltext":false,"cited_by_count":1316,"citation_normalized_percentile":{"value":0.99775624,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"34","issue":"6","first_page":"1037","last_page":"1039"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7159000039100647,"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":0.7159000039100647,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.020400000736117363,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.017999999225139618,"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/annotation","display_name":"Annotation","score":0.7807322144508362},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7542815208435059},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7241311073303223},{"id":"https://openalex.org/keywords/ensembl","display_name":"Ensembl","score":0.6855437755584717},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.609098494052887},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.5905734896659851},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5880696773529053},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5565516352653503},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5532050132751465},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4966428875923157},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.4647454619407654},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.36262133717536926},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.34745192527770996},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2965237498283386},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2770918905735016},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19920030236244202},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13456770777702332},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12491780519485474},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10225051641464233}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7807322144508362},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7542815208435059},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7241311073303223},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.6855437755584717},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.609098494052887},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.5905734896659851},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5880696773529053},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5565516352653503},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5532050132751465},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4966428875923157},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.4647454619407654},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.36262133717536926},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.34745192527770996},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2965237498283386},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2770918905735016},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19920030236244202},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13456770777702332},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12491780519485474},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10225051641464233}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btx713","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx713","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5860143","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860143","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,"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":"Bioinformatics","raw_type":"Text"},{"id":"pmid:29106469","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29106469","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx713","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx713","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.6100000143051147,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G3361386922","display_name":"Platform for Advanced Genome Science","funder_award_id":"16H06279","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1976325156","https://openalex.org/W1983922226","https://openalex.org/W2096093282","https://openalex.org/W2120141270","https://openalex.org/W2162758337","https://openalex.org/W2464319961","https://openalex.org/W2470052926","https://openalex.org/W2535055464","https://openalex.org/W2559191318","https://openalex.org/W4252553099","https://openalex.org/W6719345154"],"related_works":["https://openalex.org/W2132241624","https://openalex.org/W4392173297","https://openalex.org/W4311683883","https://openalex.org/W4212902261","https://openalex.org/W4400311305","https://openalex.org/W4221030787","https://openalex.org/W2790811106","https://openalex.org/W4385413248","https://openalex.org/W3097598351","https://openalex.org/W3111061871"],"abstract_inverted_index":{"Summary:":[0],"We":[1],"developed":[2],"a":[3,45,58,67],"prokaryotic":[4],"genome":[5,12,70],"annotation":[6,25,49,102],"pipeline,":[7],"DFAST,":[8,52],"that":[9],"also":[10,55,107,164],"supports":[11],"submission":[13],"to":[14,28,99],"public":[15],"sequence":[16],"databases.":[17],"DFAST":[18,96],"was":[19],"originally":[20],"started":[21],"as":[22,57,78],"an":[23],"on-line":[24,161],"server,":[26],"and":[27,82,105,113,122,131,137,140],"date,":[29],"over":[30],"7000":[31],"jobs":[32],"have":[33],"been":[34],"processed":[35],"since":[36],"its":[37],"first":[38],"launch":[39],"in":[40,118,128,133,156],"2016.":[41],"Here,":[42],"we":[43],"present":[44],"newly":[46],"implemented":[47,127],"background":[48],"engine":[50,64],"for":[51,110],"which":[53],"is":[54,126,144,163],"available":[56,146,165,175],"standalone":[59],"command-line":[60],"program.":[61],"The":[62,124],"new":[63,111,116],"can":[65],"annotate":[66],"typical-sized":[68],"bacterial":[69],"within":[71],"10":[72],"min,":[73],"with":[74,152],"rich":[75],"information":[76],"such":[77],"pseudogenes,":[79],"translation":[80],"exceptions":[81],"orthologous":[83],"gene":[84],"assignment":[85],"between":[86],"given":[87],"reference":[88],"genomes.":[89],"In":[90],"addition,":[91],"the":[92,101,119,149,157],"modular":[93],"framework":[94],"of":[95,115],"allows":[97],"users":[98],"customize":[100],"workflow":[103],"easily":[104],"will":[106],"facilitate":[108],"extensions":[109],"functions":[112],"incorporation":[114],"tools":[117],"future.":[120],"Availability":[121],"implementation:":[123],"software":[125,158],"Python":[129,135],"3":[130],"runs":[132],"both":[134],"2.7":[136],"3.4-on":[138],"Macintosh":[139],"Linux":[141],"systems.":[142],"It":[143],"freely":[145],"at":[147,166,176],"https://github.com/nigyta/dfast_core/under":[148],"GPLv3":[150],"license":[151],"external":[153],"binaries":[154],"bundled":[155],"distribution.":[159],"An":[160],"version":[162],"https://dfast.nig.ac.jp/.":[167],"Contact:":[168],"yn@nig.ac.jp.":[169],"Supplementary":[170,172],"information:":[171],"data":[173],"are":[174],"Bioinformatics":[177],"online.":[178]},"counts_by_year":[{"year":2026,"cited_by_count":123},{"year":2025,"cited_by_count":208},{"year":2024,"cited_by_count":232},{"year":2023,"cited_by_count":163},{"year":2022,"cited_by_count":173},{"year":2021,"cited_by_count":173},{"year":2020,"cited_by_count":133},{"year":2019,"cited_by_count":88},{"year":2018,"cited_by_count":21},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-22T07:34:49.880490","created_date":"2025-10-10T00:00:00"}
