Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

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Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

Show simple item record Pedersen, Jakob Skou Bejerano, Gill Siepel, Adam Rosenbloom, Kate Lindblad-Toh, Kerstin Lander, Eric Steven Kent, Jim Webb, Miller Haussler, David 2011-02-28T04:36:02Z 2006
dc.identifier.citation Pedersen, Jakob Skou, Gill Bejerano, Adam Siepel, Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, Jim Kent, Webb Miller, and David Haussler. 2006. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Computational Biology 2(4): e33. en_US
dc.identifier.issn 1553-734X en_US
dc.description.abstract The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general comparative genomics method based on phylogenetic stochastic context-free grammars for identifying functional RNAs encoded in the human genome and used it to survey an eight-way genome-wide alignment of the human, chimpanzee, mouse, rat, dog, chicken, zebra-fish, and puffer-fish genomes for deeply conserved functional RNAs. At a loose threshold for acceptance, this search resulted in a set of 48,479 candidate RNA structures. This screen finds a large number of known functional RNAs, including 195 miRNAs, 62 histone 3′UTR stem loops, and various types of known genetic recoding elements. Among the highest-scoring new predictions are 169 new miRNA candidates, as well as new candidate selenocysteine insertion sites, RNA editing hairpins, RNAs involved in transcript auto regulation, and many folds that form singletons or small functional RNA families of completely unknown function. While the rate of false positives in the overall set is difficult to estimate and is likely to be substantial, the results nevertheless provide evidence for many new human functional RNAs and present specific predictions to facilitate their further characterization. en_US
dc.language.iso en_US en_US
dc.publisher Public Library of Science en_US
dc.relation.isversionof doi:10.1371/journal.pcbi.0020033 en_US
dc.relation.hasversion en_US
dash.license LAA
dc.subject bioinformatics - computational biology en_US
dc.subject genetics en_US
dc.subject gene discovery en_US
dc.subject gene function en_US
dc.subject comparative genomics en_US
dc.subject evolution en_US
dc.subject molecular biology - structural biology en_US
dc.subject homo (human) en_US
dc.subject vertebrates en_US
dc.title Identification and Classification of Conserved RNA Secondary Structures in the Human Genome en_US
dc.type Journal Article en_US
dc.description.version Version of Record en_US
dc.relation.journal PLoS Computational Biology en_US Lander, Eric Steven 2011-02-28T04:36:02Z
dash.affiliation.other HMS^Systems Biology en_US

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