{"id":"https://openalex.org/W4401756121","doi":"https://doi.org/10.1186/s12859-024-05887-3","title":"HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation","display_name":"HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation","publication_year":2024,"publication_date":"2024-08-21","ids":{"openalex":"https://openalex.org/W4401756121","doi":"https://doi.org/10.1186/s12859-024-05887-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/39169276"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05887-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05887-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05887-3","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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/s12859-024-05887-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5106639473","display_name":"Lorenzo Arcioni","orcid":null},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Lorenzo Arcioni","raw_affiliation_strings":["Department of Computer Science, Sapienza University of Rome, Viale Regina Elena 295, 00166, Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Sapienza University of Rome, Viale Regina Elena 295, 00166, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092500891","display_name":"Manuel Arcieri","orcid":"https://orcid.org/0000-0002-2312-7704"},"institutions":[{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Manuel Arcieri","raw_affiliation_strings":["Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800, Kongens Lyngby, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800, Kongens Lyngby, Denmark","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026975324","display_name":"Jessica Di Martino","orcid":"https://orcid.org/0000-0003-0505-4190"},"institutions":[{"id":"https://openalex.org/I138938424","display_name":"Universit\u00e0 degli Studi della Tuscia","ror":"https://ror.org/03svwq685","country_code":"IT","type":"education","lineage":["https://openalex.org/I138938424"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Jessica Di Martino","raw_affiliation_strings":["Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Universit\u00e0 s.n.c., 01100, Viterbo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Universit\u00e0 s.n.c., 01100, Viterbo, Italy","institution_ids":["https://openalex.org/I138938424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5095904026","display_name":"Franco Liberati","orcid":null},"institutions":[{"id":"https://openalex.org/I138938424","display_name":"Universit\u00e0 degli Studi della Tuscia","ror":"https://ror.org/03svwq685","country_code":"IT","type":"education","lineage":["https://openalex.org/I138938424"]},{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Franco Liberati","raw_affiliation_strings":["Department of Computer Science, Sapienza University of Rome, Viale Regina Elena 295, 00166, Rome, Italy","Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Universit\u00e0 s.n.c., 01100, Viterbo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Sapienza University of Rome, Viale Regina Elena 295, 00166, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]},{"raw_affiliation_string":"Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Universit\u00e0 s.n.c., 01100, Viterbo, Italy","institution_ids":["https://openalex.org/I138938424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020960557","display_name":"Paolo Bottoni","orcid":"https://orcid.org/0000-0003-4662-2019"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paolo Bottoni","raw_affiliation_strings":["Department of Computer Science, Sapienza University of Rome, Viale Regina Elena 295, 00166, Rome, Italy. bottoni@di.uniroma1.it","Department of Computer Science, Sapienza University of Rome, Viale Regina Elena 295, 00166, Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Sapienza University of Rome, Viale Regina Elena 295, 00166, Rome, Italy. bottoni@di.uniroma1.it","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, Sapienza University of Rome, Viale Regina Elena 295, 00166, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086235625","display_name":"Tiziana Castrignan\u00f2","orcid":"https://orcid.org/0000-0002-0689-6720"},"institutions":[{"id":"https://openalex.org/I138938424","display_name":"Universit\u00e0 degli Studi della Tuscia","ror":"https://ror.org/03svwq685","country_code":"IT","type":"education","lineage":["https://openalex.org/I138938424"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Tiziana Castrignan\u00f2","raw_affiliation_strings":["Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Universit\u00e0 s.n.c., 01100, Viterbo, Italy. tiziana.castrignano@unitus.it","Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Universit\u00e0 s.n.c., 01100, Viterbo, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Universit\u00e0 s.n.c., 01100, Viterbo, Italy. tiziana.castrignano@unitus.it","institution_ids":[]},{"raw_affiliation_string":"Department of Ecological and Biological Sciences, University of Tuscia, Viale dell'Universit\u00e0 s.n.c., 01100, Viterbo, Italy","institution_ids":["https://openalex.org/I138938424"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5106639473"],"corresponding_institution_ids":["https://openalex.org/I861853513"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.3109,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.79938783,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"25","issue":"1","first_page":"272","last_page":"272"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8812999725341797,"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":0.8812999725341797,"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":0.014999999664723873,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.014399999752640724,"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/annotation","display_name":"Annotation","score":0.797039270401001},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7475261688232422},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.6468842625617981},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5952386856079102},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5935565829277039},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.4904894530773163},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.48185810446739197},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.45394590497016907},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.45212554931640625},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4468576908111572},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.44286638498306274},{"id":"https://openalex.org/keywords/de-novo-transcriptome-assembly","display_name":"De novo transcriptome assembly","score":0.43687379360198975},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.42172902822494507},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.4128214120864868},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37038081884384155},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3403933644294739},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33938169479370117},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.264299213886261},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19419685006141663},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18293115496635437},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17910155653953552},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16818544268608093}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.797039270401001},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7475261688232422},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6468842625617981},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5952386856079102},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5935565829277039},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.4904894530773163},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.48185810446739197},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.45394590497016907},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.45212554931640625},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4468576908111572},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.44286638498306274},{"id":"https://openalex.org/C50489715","wikidata":"https://www.wikidata.org/wiki/Q5244960","display_name":"De novo transcriptome assembly","level":5,"score":0.43687379360198975},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.42172902822494507},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.4128214120864868},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37038081884384155},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3403933644294739},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33938169479370117},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.264299213886261},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19419685006141663},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18293115496635437},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17910155653953552},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16818544268608093},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"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":"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":"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":"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-024-05887-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05887-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05887-3","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39169276","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39169276","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:11340092","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11340092","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11340092/pdf/12859_2024_Article_5887.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:f24ef9c0bacc4e249d8e5cd4f4cd3ba9","is_oa":true,"landing_page_url":"https://doaj.org/article/f24ef9c0bacc4e249d8e5cd4f4cd3ba9","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-14 (2024)","raw_type":"article"},{"id":"pmh:oai:iris.uniroma1.it:11573/1745401","is_oa":false,"landing_page_url":"https://hdl.handle.net/11573/1745401","pdf_url":null,"source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","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":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pure.atira.dk:publications/59de71ca-0164-413e-9d11-3afc49ac2d21","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/59de71ca-0164-413e-9d11-3afc49ac2d21","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Arcioni , L , Arcieri , M , Di Martino , J , Liberati , F , Bottoni , P &amp; Castrignan\u00f2 , T 2024 , ' HPC-T-Annotator : an HPC tool for de novo transcriptome assembly annotation ' , BMC Bioinformatics , vol. 25 , no. 1 , 272 . https://doi.org/10.1186/s12859-024-05887-3","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05887-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05887-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05887-3","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4401756121.pdf"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1970279759","https://openalex.org/W2003144438","https://openalex.org/W2011657487","https://openalex.org/W2018342111","https://openalex.org/W2027753686","https://openalex.org/W2045204781","https://openalex.org/W2055043387","https://openalex.org/W2055400985","https://openalex.org/W2095206320","https://openalex.org/W2096041635","https://openalex.org/W2107903949","https://openalex.org/W2153498291","https://openalex.org/W2156841387","https://openalex.org/W2422616509","https://openalex.org/W2562770483","https://openalex.org/W2590333864","https://openalex.org/W2649544508","https://openalex.org/W2779904828","https://openalex.org/W2795930404","https://openalex.org/W2804297502","https://openalex.org/W2972131171","https://openalex.org/W2980539212","https://openalex.org/W2982208012","https://openalex.org/W3030356991","https://openalex.org/W3044145717","https://openalex.org/W3080366061","https://openalex.org/W3096131779","https://openalex.org/W3110846296","https://openalex.org/W3121546362","https://openalex.org/W3143063265","https://openalex.org/W3199064813","https://openalex.org/W3205526346","https://openalex.org/W4206515897","https://openalex.org/W4213149192","https://openalex.org/W4283447531","https://openalex.org/W4303968689","https://openalex.org/W4304893247","https://openalex.org/W4308678857","https://openalex.org/W4321792474","https://openalex.org/W4353094477","https://openalex.org/W4362596286","https://openalex.org/W4378574589","https://openalex.org/W4384823408","https://openalex.org/W4384835297","https://openalex.org/W4387776415","https://openalex.org/W4390176600","https://openalex.org/W4392623515","https://openalex.org/W4395666511","https://openalex.org/W4396774718","https://openalex.org/W4399676024","https://openalex.org/W4399868382"],"related_works":["https://openalex.org/W1021674602","https://openalex.org/W2524794421","https://openalex.org/W2515779155","https://openalex.org/W2793945238","https://openalex.org/W2800773082","https://openalex.org/W1996370379","https://openalex.org/W2991935870","https://openalex.org/W2145204137","https://openalex.org/W2583890878","https://openalex.org/W2951403195"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,41,142],"availability":[2],"of":[3,15,66,156],"transcriptomic":[4],"data":[5,117,144],"for":[6,55,94,107,125],"species":[7],"without":[8,204],"a":[9,33,47,60,75,79,92,111,135,138],"reference":[10,22,76],"genome":[11],"enables":[12],"the":[13,56,64,86,115,120,154,161],"construction":[14],"de":[16,42,95,170],"novo":[17,96,171],"transcriptome":[18,28,97,172,190],"assemblies":[19],"as":[20],"alternative":[21],"resources":[23],"from":[24],"RNA-Seq":[25],"data.":[26],"A":[27],"provides":[29],"direct":[30],"information":[31],"about":[32],"species'":[34],"protein-coding":[35],"genes":[36],"under":[37],"specific":[38],"experimental":[39],"conditions.":[40],"novo\ufeff":[43],"assembly":[44],"process":[45],"produces":[46],"unigenes":[48],"file":[49],"in":[50,74,153,160,169],"FASTA":[51],"format,":[52],"subsequently":[53],"targeted":[54],"annotation.":[57],"Homology-based":[58],"annotation,":[59],"method":[61],"to":[62,202],"infer":[63],"function":[65],"sequences":[67,73],"by":[68],"estimating":[69],"similarity":[70],"with":[71],"other":[72],"database,":[77],"is":[78,127],"computationally":[80],"demanding":[81],"procedure.":[82],"RESULTS:":[83],"To":[84],"mitigate":[85],"computational":[87,183],"burden,":[88],"we":[89],"introduce":[90],"HPC-T-Annotator,":[91],"tool":[93],"homology":[98],"annotation":[99,126,168],"on":[100,134,178],"high":[101],"performance":[102],"computing":[103,123],"(HPC)":[104],"infrastructures,":[105],"designed":[106],"straightforward":[108],"configuration":[109,116],"via":[110],"Web":[112],"interface.":[113],"Once":[114],"are":[118],"given,":[119],"entire":[121],"parallel":[122],"software":[124],"automatically":[128],"generated":[129],"and":[130,185,192],"can":[131,145],"be":[132,147],"launched":[133],"supercomputer":[136],"using":[137,150],"simple":[139],"command":[140],"line.":[141],"output":[143],"then":[146],"easily":[148],"viewed":[149],"post-processing":[151],"utilities":[152],"form":[155],"Python":[157],"notebooks":[158],"integrated":[159],"proposed":[162],"software.":[163],"CONCLUSIONS:":[164],"HPC-T-Annotator":[165],"expedites":[166],"homology-based":[167],"assemblies.":[173],"Its":[174],"efficient":[175],"parallelization":[176],"strategy":[177],"HPC":[179],"infrastructures":[180],"significantly":[181],"reduces":[182],"load":[184],"execution":[186],"times,":[187],"enabling":[188],"large-scale":[189],"analysis":[191],"comparison":[193],"projects,":[194],"while":[195],"its":[196],"intuitive":[197],"graphical":[198],"interface":[199],"extends":[200],"accessibility":[201],"users":[203],"IT":[205],"skills.":[206]},"counts_by_year":[{"year":2025,"cited_by_count":6}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
