{"doi":"10.1261/rna.2210406","title":"A computational screen for mammalian pseudouridylation guide H/ACA RNAs","abstract":"<jats:p>The box H/ACA RNA gene family is one of the largest non-protein-coding gene families in eukaryotes and archaea. Recently, we developed snoGPS, a computational screening program for H/ACA snoRNAs, and applied it to <jats:italic>Saccharomyces cerevisiae</jats:italic>. We report here results of extending our method to screen for H/ACA RNAs in multiple large genomes of related species, and apply it to the human, mouse, and rat genomes. Because of the 250-fold larger search space compared to <jats:italic>S. cerevisiae</jats:italic>, significant enhancements to our algorithms were required. Complementing extensive cloning experiments performed by others, our findings include the detection and experimental verification of seven new mammalian H/ACA RNAs and the prediction of 23 new H/ACA RNA pseudouridine guide assignments. These assignments include four for H/ACA RNAs previously classified as orphan H/ACA RNAs with no known targets. We also determined systematic syntenic conservation among human and mouse H/ACA RNAs. With this work, 82 of 97 ribosomal RNA pseudouridines and 18 of 32 spliceosomal RNA pseudouridines in mammals have been linked to H/ACA guide RNAs.</jats:p>","journal":"RNA","year":2006,"id":32821,"datarank":4.346436582076475,"base_score":4.59511985013459,"endowment":4.59511985013459,"self_citation_contribution":0.6892679775201885,"citation_network_contribution":3.6571686045562863,"self_endowment_contribution":0.6892679775201885,"citer_contribution":3.6571686045562863,"corpus_percentile":null,"corpus_rank":null,"citation_count":98,"citer_count":94,"citers_with_citation_signal":85,"citers_with_endowment":85,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":173007,"name":"SERGIO BARBERAN-SOLER","orcid":null,"position":1,"is_corresponding":false},{"id":173008,"name":"TODD M. 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