{"id":"https://openalex.org/W4281753635","doi":"https://doi.org/10.1186/s12859-022-04736-5","title":"FragGeneScanRs: faster gene prediction for short reads","display_name":"FragGeneScanRs: faster gene prediction for short reads","publication_year":2022,"publication_date":"2022-05-28","ids":{"openalex":"https://openalex.org/W4281753635","doi":"https://doi.org/10.1186/s12859-022-04736-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/35643462"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04736-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04736-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04736-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04736-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084683242","display_name":"Felix Van der Jeugt","orcid":"https://orcid.org/0000-0003-3168-927X"},"institutions":[{"id":"https://openalex.org/I12607205","display_name":"HOGENT University of Applied Sciences and Arts","ror":"https://ror.org/00rs45z86","country_code":"BE","type":"education","lineage":["https://openalex.org/I12607205"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Felix Van der Jeugt","raw_affiliation_strings":["Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium. unipept@ugent.be","Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium"],"raw_orcid":"https://orcid.org/0000-0003-3168-927X","affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium. unipept@ugent.be","institution_ids":["https://openalex.org/I12607205","https://openalex.org/I32597200"]},{"raw_affiliation_string":"Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013637445","display_name":"Peter Dawyndt","orcid":"https://orcid.org/0000-0002-1623-9070"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Peter Dawyndt","raw_affiliation_strings":["Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015802960","display_name":"Bart Mesuere","orcid":"https://orcid.org/0000-0003-0610-3441"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Bart Mesuere","raw_affiliation_strings":["Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5084683242"],"corresponding_institution_ids":["https://openalex.org/I12607205","https://openalex.org/I32597200"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.801,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.85492729,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"23","issue":"1","first_page":"198","last_page":"198"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6136000156402588,"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":0.6136000156402588,"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/T10885","display_name":"Gene expression and cancer classification","score":0.2012999951839447,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.04129999876022339,"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/computer-science","display_name":"Computer science","score":0.8558061122894287},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5258337259292603},{"id":"https://openalex.org/keywords/thread","display_name":"Thread (computing)","score":0.511473536491394},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4980432987213135},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.48954591155052185},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.4529794454574585},{"id":"https://openalex.org/keywords/debugging","display_name":"Debugging","score":0.44848737120628357},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.43009430170059204},{"id":"https://openalex.org/keywords/rust","display_name":"Rust (programming language)","score":0.41115128993988037},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4031638503074646},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.37104207277297974},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.36039474606513977},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.2918485403060913}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8558061122894287},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5258337259292603},{"id":"https://openalex.org/C138101251","wikidata":"https://www.wikidata.org/wiki/Q213092","display_name":"Thread (computing)","level":2,"score":0.511473536491394},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4980432987213135},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.48954591155052185},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.4529794454574585},{"id":"https://openalex.org/C168065819","wikidata":"https://www.wikidata.org/wiki/Q845566","display_name":"Debugging","level":2,"score":0.44848737120628357},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.43009430170059204},{"id":"https://openalex.org/C197781089","wikidata":"https://www.wikidata.org/wiki/Q575650","display_name":"Rust (programming language)","level":2,"score":0.41115128993988037},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4031638503074646},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.37104207277297974},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.36039474606513977},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2918485403060913}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","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":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-022-04736-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04736-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04736-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35643462","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35643462","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9148508","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9148508","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:archive.ugent.be:8754976","is_oa":true,"landing_page_url":"http://hdl.handle.net/1854/LU-8754976","pdf_url":null,"source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1471-2105","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:99e04db18ea145f38b39027358344e10","is_oa":false,"landing_page_url":"https://doaj.org/article/99e04db18ea145f38b39027358344e10","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-8 (2022)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04736-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04736-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04736-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4268925899","display_name":"A whole new role for Unipept: a framework for comparative metaproteomics analyses","funder_award_id":"12I5220N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4281753635.pdf","grobid_xml":"https://content.openalex.org/works/W4281753635.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1822648038","https://openalex.org/W1920637681","https://openalex.org/W2038802458","https://openalex.org/W2048673910","https://openalex.org/W2069689025","https://openalex.org/W2099006507","https://openalex.org/W2120267228","https://openalex.org/W2120655738","https://openalex.org/W2147378425","https://openalex.org/W2156858199","https://openalex.org/W2162704968","https://openalex.org/W2168330474","https://openalex.org/W2418062995","https://openalex.org/W2559429800","https://openalex.org/W2572263783","https://openalex.org/W2754579667","https://openalex.org/W2758005814","https://openalex.org/W2893762247","https://openalex.org/W2945099731","https://openalex.org/W4231601595"],"related_works":["https://openalex.org/W1601811574","https://openalex.org/W1558134444","https://openalex.org/W4252135746","https://openalex.org/W128449525","https://openalex.org/W2769814451","https://openalex.org/W1587224678","https://openalex.org/W2386866874","https://openalex.org/W2914079589","https://openalex.org/W1498982577","https://openalex.org/W4220716144"],"abstract_inverted_index":{"BACKGROUND:":[0],"FragGeneScan":[1,72,98],"is":[2,22,37,43,80,93,132],"currently":[3],"the":[4,71,96,103,138],"most":[5],"accurate":[6],"and":[7,15,57,83,146],"popular":[8],"tool":[9],"for":[10,24,87,124,143],"gene":[11,73],"prediction":[12,74],"in":[13],"short":[14],"error-prone":[16],"reads,":[17],"but":[18,45],"its":[19],"execution":[20],"speed":[21],"insufficient":[23],"use":[25],"on":[26],"larger":[27],"data":[28],"sets.":[29],"The":[30,127],"parallelization":[31],"which":[32],"should":[33],"have":[34],"addressed":[35],"this":[36],"inefficient.":[38],"Its":[39,76,91],"alternative":[40],"implementation":[41,69],"FragGeneScan+":[42],"faster,":[44],"introduced":[46],"a":[47,66,118],"number":[48],"of":[49,70,130],"bugs":[50],"related":[51],"to":[52,95,102,113],"memory":[53],"management,":[54],"race":[55],"conditions":[56],"even":[58],"output":[59,92],"accuracy.":[60],"RESULTS:":[61],"This":[62],"paper":[63],"introduces":[64],"FragGeneScanRs,":[65],"faster":[67,116],"Rust":[68,128],"model.":[75],"command":[77],"line":[78],"interface":[79],"backward":[81],"compatible":[82],"adds":[84],"extra":[85],"features":[86],"more":[88],"flexible":[89],"usage.":[90],"equivalent":[94],"original":[97],"implementation.":[99],"CONCLUSIONS:":[100],"Compared":[101],"current":[104],"C":[105],"implementation,":[106],"shotgun":[107],"metagenomic":[108],"reads":[109],"are":[110],"processed":[111],"up":[112],"22":[114],"times":[115],"using":[117],"single":[119],"thread,":[120],"with":[121,141],"better":[122],"scaling":[123],"multithreaded":[125],"execution.":[126],"code":[129],"FragGeneScanRs":[131],"freely":[133],"available":[134],"from":[135],"GitHub":[136],"under":[137],"GPL-3.0":[139],"license":[140],"instructions":[142],"installation,":[144],"usage":[145],"other":[147],"documentation":[148],"(":[149],"https://github.com/unipept/FragGeneScanRs":[150],").":[151]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4}],"updated_date":"2026-08-13T07:04:57.449891","created_date":"2025-10-10T00:00:00"}
