{"id":"https://openalex.org/W2519323917","doi":"https://doi.org/10.1093/bioinformatics/btw499","title":"FARAO: the flexible all-round annotation organizer","display_name":"FARAO: the flexible all-round annotation organizer","publication_year":2016,"publication_date":"2016-08-04","ids":{"openalex":"https://openalex.org/W2519323917","doi":"https://doi.org/10.1093/bioinformatics/btw499","mag":"2519323917","pmid":"https://pubmed.ncbi.nlm.nih.gov/27493193"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw499","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw499","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/23/3664/16920340/btw499.pdf","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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/23/3664/16920340/btw499.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007616996","display_name":"Rickard Hammar\u00e9n","orcid":"https://orcid.org/0000-0001-9017-591X"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I881427289","display_name":"University of Gothenburg","ror":"https://ror.org/01tm6cn81","country_code":"SE","type":"education","lineage":["https://openalex.org/I881427289"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Rickard Hammar\u00e9n","raw_affiliation_strings":["1Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden","2Science for Life Laboratory, Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 21 Solna, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden","institution_ids":["https://openalex.org/I881427289"]},{"raw_affiliation_string":"2Science for Life Laboratory, Department of Medical Epidemiology and Biostatistics, Karolinska Institute, SE-171 21 Solna, Stockholm, Sweden","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020630476","display_name":"Chandan Pal","orcid":"https://orcid.org/0000-0002-0503-8804"},"institutions":[{"id":"https://openalex.org/I881427289","display_name":"University of Gothenburg","ror":"https://ror.org/01tm6cn81","country_code":"SE","type":"education","lineage":["https://openalex.org/I881427289"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Chandan Pal","raw_affiliation_strings":["1Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden","3Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden","institution_ids":["https://openalex.org/I881427289"]},{"raw_affiliation_string":"3Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden","institution_ids":["https://openalex.org/I881427289"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083719554","display_name":"Johan Bengtsson\u2010Palme","orcid":"https://orcid.org/0000-0002-6528-3158"},"institutions":[{"id":"https://openalex.org/I881427289","display_name":"University of Gothenburg","ror":"https://ror.org/01tm6cn81","country_code":"SE","type":"education","lineage":["https://openalex.org/I881427289"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Johan Bengtsson-Palme","raw_affiliation_strings":["1Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden","3Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden","institution_ids":["https://openalex.org/I881427289"]},{"raw_affiliation_string":"3Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden","institution_ids":["https://openalex.org/I881427289"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5083719554"],"corresponding_institution_ids":["https://openalex.org/I881427289"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5222,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.72171241,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"32","issue":"23","first_page":"3664","last_page":"3666"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.699999988079071,"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":0.699999988079071,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.03660000115633011,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.03200000151991844,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.9765790700912476},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.8255490064620972},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7320435047149658},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6093177795410156},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.5569973587989807},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.536254346370697},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.524800181388855},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5096168518066406},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.49633294343948364},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.48833104968070984},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.48717233538627625},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.47148510813713074},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4606833755970001},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.41166234016418457},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.37085312604904175},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.28697627782821655},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23558774590492249},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22208234667778015},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20467576384544373},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.159743070602417},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09423631429672241},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08015978336334229},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07974201440811157}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.9765790700912476},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8255490064620972},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7320435047149658},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6093177795410156},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.5569973587989807},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.536254346370697},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.524800181388855},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5096168518066406},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.49633294343948364},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.48833104968070984},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.48717233538627625},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.47148510813713074},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4606833755970001},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.41166234016418457},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.37085312604904175},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.28697627782821655},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23558774590492249},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22208234667778015},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20467576384544373},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.159743070602417},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09423631429672241},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08015978336334229},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07974201440811157}],"mesh":[{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btw499","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw499","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/23/3664/16920340/btw499.pdf","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27493193","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27493193","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":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw499","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw499","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/23/3664/16920340/btw499.pdf","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.44999998807907104,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1496933752","https://openalex.org/W1989348205","https://openalex.org/W2000259912","https://openalex.org/W2023270843","https://openalex.org/W2036290623","https://openalex.org/W2051443629","https://openalex.org/W2063724867","https://openalex.org/W2098466396","https://openalex.org/W2108638811","https://openalex.org/W2122270655","https://openalex.org/W2132082178","https://openalex.org/W2148683465","https://openalex.org/W2150308846","https://openalex.org/W2150491437","https://openalex.org/W2152089378","https://openalex.org/W2162576073","https://openalex.org/W2176699305"],"related_works":["https://openalex.org/W2475789275","https://openalex.org/W2745097874","https://openalex.org/W2508823388","https://openalex.org/W2225951319","https://openalex.org/W645133142","https://openalex.org/W2992663142","https://openalex.org/W1538349749","https://openalex.org/W2099352317","https://openalex.org/W4309247532","https://openalex.org/W3096946169"],"abstract_inverted_index":{"With":[0],"decreasing":[1],"costs":[2],"of":[3,44,62,68],"generating":[4],"DNA":[5],"sequence":[6],"data,":[7],"genome":[8],"and":[9,25,42,46,70,81,90],"metagenome":[10],"projects":[11],"have":[12],"become":[13],"accessible":[14],"to":[15,21],"a":[16,35],"wider":[17],"scientific":[18],"community.":[19],"However,":[20],"extract":[22],"meaningful":[23],"information":[24],"visualize":[26],"the":[27,102],"data":[28,49,55,111],"remain":[29],"challenging.":[30],"We":[31],"here":[32],"introduce":[33],"FARAO,":[34],"highly":[36],"scalable":[37],"software":[38],"for":[39,99],"organization,":[40],"visualization":[41],"integration":[43],"annotation":[45],"read":[47],"coverage":[48],"that":[50],"can":[51,64],"also":[52],"combine":[53],"output":[54],"from":[56,105],"several":[57],"bioinformatics":[58],"tools.":[59],"The":[60,92],"capabilities":[61],"FARAO":[63,76],"greatly":[65],"aid":[66],"analyses":[67],"genomic":[69],"metagenomic":[71],"datasets.":[72],"AVAILABILITY":[73],"AND":[74],"IMPLEMENTATION:":[75],"is":[77,82,96],"implemented":[78],"in":[79],"Perl":[80,93],"supported":[83],"under":[84,101],"Unix-like":[85],"operative":[86],"systems,":[87],"including":[88],"Linux":[89],"macOS.":[91],"source":[94],"code":[95],"freely":[97],"available":[98,113],"download":[100],"MIT":[103],"License":[104],"http://microbiology.se/software/farao/":[106],"CONTACT:":[107],"johan.bengtsson-palme@microbiology.seSupplementary":[108],"information:":[109],"Supplementary":[110],"are":[112],"at":[114],"Bioinformatics":[115],"online.":[116]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
