Martin Macko. Algoritmus pre hľadanie vzdialených funkčných ortológov a jeho aplikácia na OB-fold doménu. PhD thesis, Comenius University in Bratislava, 2013. Supervised by Tomáš Vinař.

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Identification of evolutionarily related proteins (orthologs) is
an important step towards understanding protein function in
living organisms. This problem is difficult in many cases because
distantly related proteins have often too divergent amino-acid
sequences, so this relation may not be identified by traditional
methods based mainly on sequence similarity. In these cases
search should use combination of structural and sequential
features of protein.  In this thesis, we propose a new approach
to the search for remote functional orthologs, where important
features of protein sequence and structure are represented by a
descriptor created by human expert. This descriptor can be used
to search for described features in candidate protein
sequences. For the problem of ortholog identification with
descriptor, we develop scoring scheme which combines sequence
profiles and support vector machines to evaluate alignment of the
descriptor to the candidate sequence, and we develop algorithms
which that the best possible alignment.  We demonstrate our
approach on the example of telomere-binding OB-fold domain. Our
method can distinguish between Telo_bind family members and
negatives, and also identifies proteins containing a related
OB-fold domain.