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GAUK 550214
rRNA Secondary Structure Prediction
2014 - 2015

Gene translation is the process of implementation of genetic information, which forms a living organism. The unit central to translation is the ribosome.

The "skeleton" (and major part) of the ribosome consists of ribosomal ribonucleic acids (rRNA), which are critical for its function. Because the function of biological molecules is mostly determined by their spatial structure, understanding the role of rRNA in translation depends on understanding rRNA structures. While rRNA nucleotide sequences can be obtained relatively easily, determining their three-dimensional structure is very demanding: sequences are known for hundreds of eucaryotic organisms while spatial structures only for 4.

An intermediate step between sequences and three-dimensional structures are secondary structures, the understanding of which enables at least partial study of rRNA behavior. Secondary structures, however, can be predicted from sequences (to an extent). The project will develop a method for predicting secondary structures of rRNA and a software infrastructure "rPredictor" (database, web interface, integrated bioinformatic tools) for making this method and an associated database of predicted structures available to the scientific community.

The rPredictor infrastructure is integral to the project because the existing database of rRNAs, SILVA, is, from a programming standpoint, insufficient and not extensible with a structure prediction module.