Ladislav Rampášek. RNA motif search in genomic sequences. Bachelor thesis, Comenius University in Bratislava, 2010. Supervised by Tomáš Vinař.
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Download from publisher: https://stella.uniba.sk/zkp-storage/dzb/dostupne/FM/2010/2010-FM-JbrpMn/
Related web page: http://compbio.fmph.uniba.sk/rnarobo/
Bibliography entry: BibTeX
The ultimate goal of this work was to develop an RNA motif search tool that, besides defects allowed by current tools (e.g. RNABob), also allows insertions and deletions in the occurrences of the motif elements. The work was motivated by practical needs of a biochemist Dr. Andrej Lupták from University of California at Irvine, who uses RNA motif search tools to discover new RNA genes of specific functions. Early in the thesis we take a more detailed look on the structure of RNA motifs and explain their role and importance. We also show how descriptors are used to define permissible deviations from the prescribed motif. To address the problem of insertions and deletions in RNA motif search, we have developed a new search tool RNAMot2 and we dedicate most of the text to its description and evaluation. The algorithm implemented in RNAMot2 consists of two parts: the new algorithm for search of individual motif elements based on dynamic programing, and the backtracking algorithm used in an existing tool RNAMot. RNAMot2 uses motif descriptors compatible with RNABob, that we have extended to handle insertions. Our empirical results have shown that RNAMot2 can be more sensitive than current tools due to the ability to allow insertions and deletions, however is much slower. Nevertheless, in the end of the thesis we propose several ways how to significantly enhance the RNAMot2 time performance in the future.