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gRNAid : a tool for the comparative analysis of RNA secondary structures

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https://ir.library.oregonstate.edu/concern/graduate_projects/9w032b29w

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  • The secondary structure of a 16S rRNA molecule is a graphical, two dimensional representation used by molecular biologists in determining evolutionary relationships between different organisms. By comparing two secondary structures, scientists can obtain knowledge of how 'related' one species of bacteria may be to another species [OLSE 1986]. To date, there is no widely used computer program for secondary structure creation because these programs generally do not work well with large sets of sequence data. In other words, these programs work adequately on small RNA fragments, but tend to create incorrect or unwieldy secondary structures on larger data sets. Thus, the molecular biologist is forced to create the secondary structure by hand, which is a monotonous and time consuming task. The gRNAid program is a tool implemented for the Macintosh that will aid in the creation of secondary structures. Rather than trying to calculate the molecular bonding in order to form the structure, gRNAid looks at a known secondary structure and uses it as a template to create a new secondary structure for another organism.
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