{"id":"https://openalex.org/W4283590022","doi":"https://doi.org/10.1093/bib/bbac235","title":"Virus finding tools: current solutions and limitations","display_name":"Virus finding tools: current solutions and limitations","publication_year":2022,"publication_date":"2022-06-26","ids":{"openalex":"https://openalex.org/W4283590022","doi":"https://doi.org/10.1093/bib/bbac235","pmid":"https://pubmed.ncbi.nlm.nih.gov/35753694"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac235","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac235","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024493121","display_name":"Grete Francesca Privitera","orcid":"https://orcid.org/0000-0003-1807-4780"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Grete Francesca Privitera","raw_affiliation_strings":["Department of Physics and Astronomy, University of Catania , Viale A. Doria, 6, 95125, Catania , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, University of Catania , Viale A. Doria, 6, 95125, Catania , Italy","institution_ids":["https://openalex.org/I39063666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023263135","display_name":"Salvatore Alaimo","orcid":"https://orcid.org/0000-0003-4825-7617"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Salvatore Alaimo","raw_affiliation_strings":["Department of Clinical and Experimental Medicine, University of Catania , c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical and Experimental Medicine, University of Catania , c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania , Italy","institution_ids":["https://openalex.org/I39063666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000272110","display_name":"Alfredo Ferro","orcid":"https://orcid.org/0000-0002-9431-5788"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alfredo Ferro","raw_affiliation_strings":["Department of Clinical and Experimental Medicine, University of Catania , c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical and Experimental Medicine, University of Catania , c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania , Italy","institution_ids":["https://openalex.org/I39063666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057481978","display_name":"Alfredo Pulvirenti","orcid":"https://orcid.org/0000-0002-9764-0295"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Alfredo Pulvirenti","raw_affiliation_strings":["Department of Clinical and Experimental Medicine, University of Catania , c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical and Experimental Medicine, University of Catania , c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania , Italy","institution_ids":["https://openalex.org/I39063666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5057481978"],"corresponding_institution_ids":["https://openalex.org/I39063666"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.6941,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.83505389,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"23","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.8468000292778015,"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":0.8468000292778015,"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/T11495","display_name":"Animal Virus Infections Studies","score":0.06520000100135803,"subfield":{"id":"https://openalex.org/subfields/1103","display_name":"Animal Science and Zoology"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.022700000554323196,"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/current","display_name":"Current (fluid)","score":0.7188792824745178},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5393857955932617},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.41574549674987793},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2076447606086731},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09338662028312683},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.06845876574516296},{"id":"https://openalex.org/keywords/infectious-disease","display_name":"Infectious disease (medical specialty)","score":0.05087283253669739}],"concepts":[{"id":"https://openalex.org/C148043351","wikidata":"https://www.wikidata.org/wiki/Q4456944","display_name":"Current (fluid)","level":2,"score":0.7188792824745178},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5393857955932617},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.41574549674987793},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2076447606086731},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09338662028312683},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.06845876574516296},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.05087283253669739},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac235","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac235","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35753694","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35753694","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W1519422934","https://openalex.org/W1973738093","https://openalex.org/W1973862547","https://openalex.org/W1975375203","https://openalex.org/W1983259930","https://openalex.org/W1987408256","https://openalex.org/W1995320511","https://openalex.org/W2003347102","https://openalex.org/W2013544175","https://openalex.org/W2020541351","https://openalex.org/W2021724381","https://openalex.org/W2035322315","https://openalex.org/W2036897871","https://openalex.org/W2046159909","https://openalex.org/W2053057991","https://openalex.org/W2080277009","https://openalex.org/W2098521327","https://openalex.org/W2103441770","https://openalex.org/W2106245031","https://openalex.org/W2118258530","https://openalex.org/W2122231878","https://openalex.org/W2124985265","https://openalex.org/W2126419817","https://openalex.org/W2131271579","https://openalex.org/W2140729960","https://openalex.org/W2141920662","https://openalex.org/W2142678031","https://openalex.org/W2144560237","https://openalex.org/W2158274053","https://openalex.org/W2159954944","https://openalex.org/W2161488606","https://openalex.org/W2167237593","https://openalex.org/W2167511301","https://openalex.org/W2169145121","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2170855681","https://openalex.org/W2337982522","https://openalex.org/W2504173038","https://openalex.org/W2528456062","https://openalex.org/W2535722386","https://openalex.org/W2565824505","https://openalex.org/W2587382807","https://openalex.org/W2603488895","https://openalex.org/W2801905545","https://openalex.org/W2805540097","https://openalex.org/W2913426519","https://openalex.org/W2949351818","https://openalex.org/W2949680846","https://openalex.org/W2961387603","https://openalex.org/W2963276645","https://openalex.org/W2985444402","https://openalex.org/W2990618091","https://openalex.org/W3004279987","https://openalex.org/W3101767322","https://openalex.org/W3102588302","https://openalex.org/W3128962620","https://openalex.org/W3131055609","https://openalex.org/W3152668224","https://openalex.org/W4236236547","https://openalex.org/W4293088719","https://openalex.org/W4293196852","https://openalex.org/W6659183976","https://openalex.org/W6683504902","https://openalex.org/W6728743016","https://openalex.org/W6751659378","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4382894326","https://openalex.org/W3035105474","https://openalex.org/W2390279801","https://openalex.org/W4205698903","https://openalex.org/W2358668433","https://openalex.org/W4294968941","https://openalex.org/W4283819461","https://openalex.org/W4390279739","https://openalex.org/W2376932109"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,23],"study":[2],"of":[3,46,80,93,121,146,156,170],"the":[4,17,47,78,110,113,133,141],"Human":[5],"Virome":[6],"remains":[7],"challenging":[8],"nowadays.":[9],"Viral":[10],"metagenomics,":[11],"through":[12,140],"high-throughput":[13],"sequencing":[14],"data,":[15],"is":[16,26,40],"best":[18],"choice":[19,130],"for":[20,32,77],"virus":[21],"discovery.":[22],"metagenomics":[24,51],"approach":[25],"culture-independent":[27],"and":[28,64,96,126,128,143],"sequence-independent,":[29],"helping":[30],"search":[31],"either":[33],"known":[34],"or":[35,165],"novel":[36],"viruses.":[37],"Though":[38],"it":[39],"estimated":[41],"that":[42,103,119],"more":[43],"than":[44],"40%":[45],"viruses":[48,66,81,95,111],"found":[49,151,161],"in":[50,67,82,107,112,162],"analysis":[52,101,148,172],"are":[53],"not":[54],"recognizable,":[55],"we":[56,116],"decided":[57],"to":[58,62],"analyze":[59],"several":[60],"tools":[61,86,123],"identify":[63],"discover":[65],"RNA-seq":[68,83],"samples.":[69],"RESULTS:":[70],"We":[71],"have":[72],"analyzed":[73],"eight":[74],"Virus":[75],"Tools":[76],"identification":[79],"data.":[84],"These":[85],"were":[87],"compared":[88],"using":[89],"a":[90,97],"synthetic":[91],"dataset":[92],"30":[94],"real":[98,157],"one.":[99],"Our":[100],"shows":[102],"no":[104],"tool":[105],"succeeds":[106],"recognizing":[108],"all":[109],"datasets.":[114],"So":[115],"can":[117,149,159,173],"conclude":[118],"each":[120],"these":[122],"has":[124],"pros":[125],"cons,":[127],"their":[129,147,171],"depends":[131],"on":[132],"application":[134],"domain.":[135],"AVAILABILITY:":[136],"Synthetic":[137],"data":[138,158],"used":[139],"review":[142],"raw":[144],"results":[145,169],"be":[150,160,174],"at":[152],"https://zenodo.org/record/6426147.":[153],"FASTQ":[154],"files":[155],"GEO":[163],"(https://www.ncbi.nlm.nih.gov/gds)":[164],"ENA":[166],"(https://www.ebi.ac.uk/ena/browser/home).":[167],"Raw":[168],"downloaded":[175],"from":[176],"https://zenodo.org/record/6425917.":[177]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
