Abstract

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. One of the most powerful sequence analysis techniques used for identifying
and annotating the biological sequences is “Multiple Sequence Alignment” (MSA). 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 and adjust the strategy applied by TMCoffee, a 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.