Obhajoba dizertačnej práce

Thu 21 Mar. 2013, 13:00

Title: Algoritmus pre hľadanie vzdialených funkčných ortológov a jeho aplikácia na OB-fold doménu
Speaker: Martin Macko

Identification of evolutionarily related proteins (orthologs) is an important step
towards understanding protein function in living organisms. This problem is
dicult 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 prop ose 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.