Master Thesis Defense: Akhil Jobby
Speaker: Akhil Jobby
Supervisor: Dr. G. Butler
Drs. T. Glatard, A. Hanna, T.-H. Chen (Chair)
Title: Multiple Sequence Alignment of Transmembrane Beta-barrel Proteins
Date:Wednesday, August 21, 2019
Place: EV 2.184
The two main types of Transmembrane proteins are Transmembrane alpha helices (TMAH) and Transmembrane beta-barrels (TMBB). From literature, we know that both are responsible for diverse biologically important functions. Since there is plenty of sequence and structural data available on various TMAH proteins, many techniques have been developed to analyze their sequence. On the contrary, not many TMBB proteins have been identified or studied upon. One of the most powerful sequence analysis techniques used for identifying and annotating the biological sequences is “Multiple Sequence Alignment” (MSA). Thus, it is often used for phylogenetic analysis, identification of conserved regions in the sequences, prediction of the topology of proteins, etc.
High-throughput sequencing methods generate huge volume of sequence data, but they remain largely unannotated. Hence an MSA method for TMBB would be important for sequence-based studies and identifying more of such proteins. In this thesis, we apply a method called homology extension to the MSA of TMBB. Our method adjusts the strategy applied by TM-Coffee (state of the art MSA method tested for TMAH) to make it suitable for TMBB proteins. We focus on extensively evaluating this method and comparing it with popular MSA tools.