Searching for non-coding RNAs in genomic sequences using ncRNAscout

Recently non-coding RNA (ncRNA) genes have been found to serve many important functions in the cell such as regulation of gene expression at the transcriptional level. Potentially there are more ncRNA molecules yet to be found and their possible functions are to be revealed. The discovery of ncRNAs is a difficult task because they lack sequence indicators such as the start and stop codons displayed by protein-coding RNAs. Current methods utilize either sequence motifs or structural parameters to detect novel ncRNAs within genomes. Here, we present an ab initio ncRNA finder, named ncRNAscout, by utilizing both sequence motifs and structural parameters. Specifically, our method has three components: (i) a measure of the frequency of a sequence, (ii) a measure of the structural stability of a sequence contained in a t-score, and (iii) a measure of the frequency of certain patterns within a sequence that may indicate the presence of ncRNA. Experimental results show that, given a genome and a set of known ncRNAs, our method is able to accurately identify and locate a significant number of ncRNA sequences in the genome. The ncRNAscout tool is available for downloading at http://bioinformatics.njit.edu/ncRNAscout.