Discovering cis-regulatory RNAs in Shewanella genomes by Support Vector Machines.

ABSTRACT: An increasing number of cis-regulatory RNA elements have been found to regulate gene expression post-transcriptionally in various biological processes in bacterial systems. Effective computational tools for large-scale identification of novel regulatory RNAs are strongly desired to facilitate our exploration of gene regulation mechanisms and regulatory networks. We present a new computational program named RSSVM (RNA Sampler+Support Vector Machine), which employs Support Vector Machines (SVMs) for efficient identification of functional RNA motifs from random RNA secondary structures. RSSVM uses a set of distinctive features to represent the common RNA secondary structure and structural alignment predicted by RNA Sampler, a tool for accurate common RNA secondary structure prediction, and is

SUBMITTER: Xu X 

PROVIDER: S-EPMC2659441 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature