{"id":"https://openalex.org/W7126429928","doi":"https://doi.org/10.1186/s12859-026-06380-9","title":"piRAT: piRNA Annotation Tool for annotating, analyzing, and visualizing piRNAs","display_name":"piRAT: piRNA Annotation Tool for annotating, analyzing, and visualizing piRNAs","publication_year":2026,"publication_date":"2026-01-31","ids":{"openalex":"https://openalex.org/W7126429928","doi":"https://doi.org/10.1186/s12859-026-06380-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/41620686"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-026-06380-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06380-9","pdf_url":null,"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://doi.org/10.1186/s12859-026-06380-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107739271","display_name":"Dominik Robak","orcid":null},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Dominik Robak","raw_affiliation_strings":["Laboratory of Bioinformatics and Genome Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krak\u00f3w, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Genome Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krak\u00f3w, Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052750731","display_name":"Guillem Ylla","orcid":"https://orcid.org/0000-0003-4540-0131"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Guillem Ylla","raw_affiliation_strings":["Laboratory of Bioinformatics and Genome Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krak\u00f3w, Poland. guillem.ylla@uj.edu.pl"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Genome Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krak\u00f3w, Poland. guillem.ylla@uj.edu.pl","institution_ids":["https://openalex.org/I126596746"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5052750731"],"corresponding_institution_ids":["https://openalex.org/I126596746"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":5.0259,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.9039909,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"27","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9635000228881836,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9635000228881836,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"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/T10062","display_name":"MicroRNA in disease regulation","score":0.007799999788403511,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.0017999999690800905,"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/piwi-interacting-rna","display_name":"Piwi-interacting RNA","score":0.9128999710083008},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7985000014305115},{"id":"https://openalex.org/keywords/germline","display_name":"Germline","score":0.4099000096321106},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.3862999975681305},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.3779999911785126}],"concepts":[{"id":"https://openalex.org/C147724379","wikidata":"https://www.wikidata.org/wiki/Q2367421","display_name":"Piwi-interacting RNA","level":5,"score":0.9128999710083008},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7985000014305115},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6498000025749207},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5504000186920166},{"id":"https://openalex.org/C109825262","wikidata":"https://www.wikidata.org/wiki/Q1139164","display_name":"Germline","level":3,"score":0.4099000096321106},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.3862999975681305},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.3779999911785126},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36809998750686646},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3653999865055084},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.2793000042438507},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26179999113082886},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.2538999915122986}],"mesh":[{"descriptor_ui":"D000094322","descriptor_name":"Piwi-Interacting RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000094322","descriptor_name":"Piwi-Interacting RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","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}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-026-06380-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06380-9","pdf_url":null,"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:41620686","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41620686","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":"Journal Article"},{"id":"pmh:oai:ruj.uj.edu.pl:item/570307","is_oa":true,"landing_page_url":"https://ruj.uj.edu.pl/handle/item/570307","pdf_url":"http://ruj.uj.edu.pl/bitstreams/58a6c5c5-c5c5-44e4-815d-33c1565ac578/download","source":{"id":"https://openalex.org/S4306401249","display_name":"Jagiellonian University Repository (Jagiellonian University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I126596746","host_organization_name":"Jagiellonian University","host_organization_lineage":["https://openalex.org/I126596746"],"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":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:ea8c208ce8954a4eaf45adab1b5ffad9","is_oa":false,"landing_page_url":"https://doaj.org/article/ea8c208ce8954a4eaf45adab1b5ffad9","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 27, Iss 1 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12947357","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12947357/","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-026-06380-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06380-9","pdf_url":null,"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":[{"id":"https://openalex.org/G8716337596","display_name":null,"funder_award_id":"UMO-2021/43/D/NZ2/03228","funder_id":"https://openalex.org/F4320322650","funder_display_name":"Narodowym Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320322650","display_name":"Narodowym Centrum Nauki","ror":"https://ror.org/03ha2q922"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1971549481","https://openalex.org/W1976342457","https://openalex.org/W1977733607","https://openalex.org/W2025635760","https://openalex.org/W2026685039","https://openalex.org/W2040975355","https://openalex.org/W2046318418","https://openalex.org/W2050385516","https://openalex.org/W2065669787","https://openalex.org/W2077879161","https://openalex.org/W2085421027","https://openalex.org/W2107602656","https://openalex.org/W2128746033","https://openalex.org/W2157334713","https://openalex.org/W2279483750","https://openalex.org/W2773195131","https://openalex.org/W2777208796","https://openalex.org/W2839756788","https://openalex.org/W2865530545","https://openalex.org/W2890857184","https://openalex.org/W2907590003","https://openalex.org/W2968344903","https://openalex.org/W3087026888","https://openalex.org/W3132727471","https://openalex.org/W3171485191","https://openalex.org/W3191485155","https://openalex.org/W3204378293","https://openalex.org/W4210403164","https://openalex.org/W4221055196","https://openalex.org/W4403110793"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1,106],"recent":[2],"years,":[3],"Piwi-interacting":[4],"RNAs":[5],"(piRNAs)":[6],"have":[7],"been":[8],"found":[9],"to":[10,84,98],"be":[11],"involved":[12],"in":[13,22,118],"different":[14],"biological":[15],"roles":[16],"beyond":[17],"their":[18,38],"initially":[19],"identified":[20],"role":[21],"protecting":[23],"the":[24,76,113,135],"germline":[25],"genome.":[26,86],"However,":[27],"there":[28],"is":[29,150],"a":[30,59,85,151],"lack":[31],"of":[32,49,120,127],"robust":[33],"computational":[34],"tools":[35],"that":[36],"facilitate":[37],"accurate":[39],"annotation,":[40],"analysis,":[41],"and":[42,53,71,92,101,130,133],"visualization,":[43],"which":[44],"would":[45],"allow":[46],"large-scale":[47],"analysis":[48],"piRNAs":[50,67,73],"across":[51],"samples":[52],"species.":[54],"RESULTS:":[55],"We":[56],"present":[57],"piRAT,":[58],"piRNA":[60,69,128],"Annotation":[61],"Tool":[62],"for":[63,154,158],"annotating":[64],"both":[65],"primary":[66],"from":[68],"clusters":[70,129],"secondary":[72],"generated":[74,134],"via":[75],"ping-pong":[77,131],"cycle,":[78],"using":[79],"small":[80],"RNA-seq":[81],"data":[82,147],"mapped":[83],"piRAT":[87,110,140],"also":[88],"performs":[89],"descriptive":[90],"analyses":[91],"generates":[93],"comprehensive":[94,115],"reports":[95],"with":[96],"visualizations":[97],"support":[99],"annotations":[100,126,144],"provide":[102],"further":[103],"insights.":[104],"CONCLUSIONS:":[105],"our":[107],"comparative":[108],"analyses,":[109],"emerged":[111],"as":[112],"most":[114,136],"tool":[116],"available":[117],"terms":[119],"functionalities.":[121],"It":[122],"consistently":[123],"produced":[124],"higher-quality":[125],"sites":[132],"detailed":[137],"reports.":[138],"As":[139],"requires":[141],"no":[142],"prior":[143],"or":[145],"special":[146],"preprocessing,":[148],"it":[149],"versatile":[152],"choice":[153],"any":[155],"species,":[156],"particularly":[157],"non-model":[159],"organisms.":[160]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-08-23T07:36:19.812096","created_date":"2026-02-02T00:00:00"}
