{"id":"https://openalex.org/W2100363512","doi":"https://doi.org/10.1093/nar/gkr485","title":"PHAST: A Fast Phage Search Tool","display_name":"PHAST: A Fast Phage Search Tool","publication_year":2011,"publication_date":"2011-06-14","ids":{"openalex":"https://openalex.org/W2100363512","doi":"https://doi.org/10.1093/nar/gkr485","mag":"2100363512","pmid":"https://pubmed.ncbi.nlm.nih.gov/21672955"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkr485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr485","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W347/7631619/gkr485.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,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/nar/article-pdf/39/suppl_2/W347/7631619/gkr485.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073467023","display_name":"You Zhou","orcid":"https://orcid.org/0000-0002-7081-921X"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Y. Zhou","raw_affiliation_strings":["Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8","institution_ids":["https://openalex.org/I154425047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066819567","display_name":"Yong Liang","orcid":"https://orcid.org/0000-0002-3702-3113"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]},{"id":"https://openalex.org/I40752897","display_name":"National Institute for Nanotechnology","ror":"https://ror.org/05c0g2426","country_code":"CA","type":"facility","lineage":["https://openalex.org/I40752897","https://openalex.org/I4210159778"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Y. Liang","raw_affiliation_strings":["Department of Biological Sciences, 2 Department of Computing Science, University of Alberta and 3 National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, 2 Department of Computing Science, University of Alberta and 3 National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8","institution_ids":["https://openalex.org/I154425047","https://openalex.org/I40752897"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009079272","display_name":"Karlene H. Lynch","orcid":"https://orcid.org/0009-0008-6552-993X"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]},{"id":"https://openalex.org/I40752897","display_name":"National Institute for Nanotechnology","ror":"https://ror.org/05c0g2426","country_code":"CA","type":"facility","lineage":["https://openalex.org/I40752897","https://openalex.org/I4210159778"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"K. H. Lynch","raw_affiliation_strings":["Department of Biological Sciences, 2 Department of Computing Science, University of Alberta and 3 National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, 2 Department of Computing Science, University of Alberta and 3 National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8","institution_ids":["https://openalex.org/I154425047","https://openalex.org/I40752897"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077747318","display_name":"Jonathan J. Dennis","orcid":"https://orcid.org/0000-0002-3925-9533"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]},{"id":"https://openalex.org/I40752897","display_name":"National Institute for Nanotechnology","ror":"https://ror.org/05c0g2426","country_code":"CA","type":"facility","lineage":["https://openalex.org/I40752897","https://openalex.org/I4210159778"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"J. J. Dennis","raw_affiliation_strings":["Department of Biological Sciences, 2 Department of Computing Science, University of Alberta and 3 National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, 2 Department of Computing Science, University of Alberta and 3 National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8","institution_ids":["https://openalex.org/I154425047","https://openalex.org/I40752897"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003573061","display_name":"David S. Wishart","orcid":"https://orcid.org/0000-0002-3207-2434"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]},{"id":"https://openalex.org/I40752897","display_name":"National Institute for Nanotechnology","ror":"https://ror.org/05c0g2426","country_code":"CA","type":"facility","lineage":["https://openalex.org/I40752897","https://openalex.org/I4210159778"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"D. S. Wishart","raw_affiliation_strings":["Department of Biological Sciences, 2 Department of Computing Science, University of Alberta and 3 National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, 2 Department of Computing Science, University of Alberta and 3 National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8","institution_ids":["https://openalex.org/I154425047","https://openalex.org/I40752897"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5003573061"],"corresponding_institution_ids":["https://openalex.org/I154425047","https://openalex.org/I40752897"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":51.5916,"has_fulltext":true,"cited_by_count":2111,"citation_normalized_percentile":{"value":0.9996591,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"39","issue":"suppl","first_page":"W347","last_page":"W352"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9972000122070312,"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/T11688","display_name":"Microbial infections and disease research","score":0.9925000071525574,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/prophage","display_name":"Prophage","score":0.9833602905273438},{"id":"https://openalex.org/keywords/genbank","display_name":"GenBank","score":0.9082439541816711},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7666541337966919},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.585228681564331},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.49411752820014954},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.4529120922088623},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3928264379501343},{"id":"https://openalex.org/keywords/bacteriophage","display_name":"Bacteriophage","score":0.17759054899215698},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14469274878501892}],"concepts":[{"id":"https://openalex.org/C73445445","wikidata":"https://www.wikidata.org/wiki/Q1712327","display_name":"Prophage","level":5,"score":0.9833602905273438},{"id":"https://openalex.org/C79029880","wikidata":"https://www.wikidata.org/wiki/Q901755","display_name":"GenBank","level":3,"score":0.9082439541816711},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7666541337966919},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.585228681564331},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.49411752820014954},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4529120922088623},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3928264379501343},{"id":"https://openalex.org/C2776441376","wikidata":"https://www.wikidata.org/wiki/Q165028","display_name":"Bacteriophage","level":4,"score":0.17759054899215698},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14469274878501892},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0}],"mesh":[{"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":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","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":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},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkr485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr485","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W347/7631619/gkr485.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,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:21672955","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21672955","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:cisti-icist.nrc-cnrc.ca:cistinparc:21271535","is_oa":false,"landing_page_url":"https://nrc-publications.canada.ca/eng/view/object/?id=f4eed25d-c4d4-4c89-ab4c-3d7e5ec82f75","pdf_url":null,"source":{"id":"https://openalex.org/S7407055245","display_name":"NPARC","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3125810","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3125810","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":null,"license_id":null,"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/gkr485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr485","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W347/7631619/gkr485.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,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320326646","display_name":"Genome Alberta","ror":null},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100363512.pdf","grobid_xml":"https://content.openalex.org/works/W2100363512.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W171943169","https://openalex.org/W204992930","https://openalex.org/W1673310716","https://openalex.org/W1921607560","https://openalex.org/W1971178500","https://openalex.org/W1988102426","https://openalex.org/W1996053875","https://openalex.org/W2012049965","https://openalex.org/W2032870665","https://openalex.org/W2054920102","https://openalex.org/W2079934389","https://openalex.org/W2083473010","https://openalex.org/W2141394464","https://openalex.org/W2149429041","https://openalex.org/W2151289717","https://openalex.org/W2158406706","https://openalex.org/W2158714788","https://openalex.org/W2163781727"],"related_works":["https://openalex.org/W2100363512","https://openalex.org/W2562911651","https://openalex.org/W2279684808","https://openalex.org/W3137911940","https://openalex.org/W3217304749","https://openalex.org/W2894932706","https://openalex.org/W2066142713","https://openalex.org/W2767606877","https://openalex.org/W1673028544","https://openalex.org/W2582968398"],"abstract_inverted_index":{"PHAge":[0],"Search":[1],"Tool":[2],"(PHAST)":[3],"is":[4,71,84,138],"a":[5,41],"web":[6],"server":[7],"designed":[8],"to":[9,54,65,73,79,87],"rapidly":[10,39],"and":[11,15,38,57,61,77,89,96,106,109,113,133],"accurately":[12],"identify,":[13],"annotate":[14,56,90],"graphically":[16],"display":[17,58,125],"prophage":[18,59,62,67,104,107,128],"sequences":[19,60],"within":[20],"bacterial":[21],"genomes":[22],"or":[23,32],"plasmids.":[24],"It":[25,83],"accepts":[26],"either":[27],"raw":[28,92],"DNA":[29,93],"sequence":[30,94],"data":[31,37,95],"partially":[33],"annotated":[34,101],"GenBank":[35],"formatted":[36],"performs":[40],"number":[42],"of":[43],"database":[44],"comparisons":[45],"as":[46,48],"well":[47],"phage":[49],"'cornerstone'":[50],"feature":[51],"identification":[52,68],"steps":[53],"locate,":[55],"features.":[63],"Relative":[64],"other":[66],"tools,":[69],"PHAST":[70,116,137],"up":[72,78],"40":[74],"times":[75],"faster":[76],"15%":[80],"more":[81],"sensitive.":[82],"also":[85,117],"able":[86],"process":[88],"both":[91,131],"Genbank":[97],"files,":[98],"provide":[99],"richly":[100],"tables":[102],"on":[103],"features":[105],"'quality'":[108],"distinguish":[110],"between":[111],"intact":[112],"incomplete":[114],"prophage.":[115],"generates":[118],"downloadable,":[119],"high":[120],"quality,":[121],"interactive":[122],"graphics":[123],"that":[124],"all":[126],"identified":[127],"components":[129],"in":[130],"circular":[132],"linear":[134],"genomic":[135],"views.":[136],"available":[139],"at":[140],"(http://phast.wishartlab.com).":[141]},"counts_by_year":[{"year":2026,"cited_by_count":35},{"year":2025,"cited_by_count":86},{"year":2024,"cited_by_count":130},{"year":2023,"cited_by_count":108},{"year":2022,"cited_by_count":164},{"year":2021,"cited_by_count":162},{"year":2020,"cited_by_count":183},{"year":2019,"cited_by_count":182},{"year":2018,"cited_by_count":211},{"year":2017,"cited_by_count":237},{"year":2016,"cited_by_count":247},{"year":2015,"cited_by_count":180},{"year":2014,"cited_by_count":115},{"year":2013,"cited_by_count":55},{"year":2012,"cited_by_count":14}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
