New tools for exploring noncoding RNA-mediated regulatory networksS.Stanley1
We have developed a new application, which provides an integrated platform for the isolation from genomes of complete sets of primary sequence repeats at any desired length, as well as providing methods for growing those repeats to arbitrary length, with emphasis on parallelizability and provability. Functional annotations, secondary RNA structure predictions, gene expression, and other data are connected to sequence matches based on their nearest known genetic features. A web based query interface enables the creation of subsets of the complete sequence matches set by applying multiple filters such as sequence composition, functional designation, translational status, phenotype, expression status, etc., and creates a browsable index to facilitate perusal of secondary structure predictions, functionally grouped expression data, associated public annotation information and multiple statistics for the matches, and then provides an annotation interface allowing researchers to share insights on cached query sets. We have utilized this system to examine the set of subsequences of meiotic introns matched elsewhere in the Saccharomyces cerevisiae genome to find candidates for sequence-dependent RNA-mediated gene regulation and note a distinct bias toward functionally related features.