Examining stem-loops as a sequence signal for identifying structural RNA genes

This project examines stem-loops as a means to identify structural RNA genes along genomic sequences. To undertake this task, an algorithm was developed to scan genomic sequences for stem-loops similar to those typically found in ribosomal RNA. Each stem-loop is quantified with metrics which measure length and spacing attributes. With the help of annotated genomes, we are able to calculate the mean metric values in the various domains which make up the genome. This includes coding sequences, non-coding DNA, ribosomal RNAs, and transfer RNAs. Subsequently, these values are evaluated for their ability to distinguish structural RNAs from their genomic counterparts. Our results indicate that some stem-loop metrics are capable of identifying ribosomal RNA genes in genomes across a wide range of G+C content levels. These results merit further study into this novel approach.