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Abstract:
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n the first part of this dissertation different repeat types are defined
as well as repeats that satisfy motif masks. A method for precise repeat finding
in input sequences of arbitrary length has been described. As the input sequences
can be very long, the number of found repeats can also be large. For that reason
it is important that the method also includes filtering found repeats based on the
expected number of their occurrences.
The method was first applied to protein sequences in which experimentally
confirmed T-cell epitopes from the IEDB database were registered. Association
rules were applied to the found repeats in order to construct a model that would
enable the prediction of the positions of T-cell epitopes in protein sequences.
In this way, it would indicate to researchers a region in the protein sequence
where an epitope can be expected with high confidence. In the case of T-cell
epitopes, a large number of rules with high confidence was found. These rules can
be considered as reliable predictors of the position of T-cell epitopes within the
protein sequences. Based on the results found, association rules were formed that
characterize the epitopes and the repeats associated with them in more detail. As
a large number of results were found, only their part is presented in this disser-
tation. On the basis of the strings that determine the repeat, a motif mask that
the repeat needs to satisfy was searched for. The entire procedure was applied to
both direct non-complementary repeats and indirect non-complementary repeats.
With similar results, the entire procedure was applied to B-cell epitopes on data
from the IEDB database.
Data on experimentally confirmed short linear motifs were taken from the ELM
database. In protein sequences where short linear motifs were registered, repeats
were searched for and association rules were applied to them. The rules with high
confidence have been singled out in particular. On the basis of the results found,
motif masks that repeats with high confidence would satisfy were searched for. |