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.

Article A user interface for accessing 3D content on the World Wide Web Share on Authors: Mike Mohageg Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CA Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CAView Profile , Rob Myers Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CA Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CAView Profile , Chris Marrin Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CA Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CAView Profile , Jim Kent Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CA Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CAView Profile , David Mott Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CA Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CAView Profile , Paul Isaacs Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CA Silicon Graphics, Inc., 2011 N. Shoreline Blvd., Mountain View, CAView Profile Authors Info & Claims CHI '96: Proceedings of the SIGCHI Conference on Human Factors in Computing SystemsApril 1996 Pages 466–ff.https://doi.org/10.1145/238386.238608Published:13 April 1996 9citation713DownloadsMetricsTotal Citations9Total Downloads713Last 12 Months6Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access