Ladislav Rampášek. RNA motif search in genomic sequences. Bachelor thesis, Comenius University in Bratislava, 2010. Supervised by Tomáš Vinař.

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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.