Ralph Pethica - Alumni
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Project Information
- Supervisor: Dr Julian Gough
- Started: October 2007
- Funding: EPSRC Departmental Grant
- Research: Using computational methods to investigate the ways in which new families of protein domains evolve.
- Description: Proteins, the building blocks of organisms can be broken down into one or more structural domains. If there is structural, functional and sequence evidence for a common ancestor, these protein domains are said to belong to the same superfamily. Within a superfamily, domains can be grouped into families, where amino acid sequences or common features are present. We are interested in the ways in which new families evolve, and the environmental pressures, which cause this to happen. This work will rely on exploring the established SCOP and SUPERFAMILY databases using computational methods to build on our understanding of the evolutionary processes at work.
Software
TreeVector - Integrated Phylogenetic Trees Using SVG
TreeVector is a utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files.
It is installed on the SUPERFAMILY server and can be used to plot protein domain architectures trees to display relationships between any set of fully sequenced genomes.
Publications
- Wilson, D., Pethica, R., Zhou, Y., Talbot, C., Vogel, C., Madera, M., Chothia, C. and Gough, J. (2009) SUPERFAMILY-sophisticated comparative genomics, data mining, visualization and phylogeny. Nucl. Acids Res. 37, D380-D386. PDF
- Pethica, R., Barker, G., Kovacs, T. and Gough, J. (2010) TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web. PLoS ONE 5(1), e8934. PDF
- de Lima Morais, D., Fang, H., Rackham, O.J.L., Wilson, D., Pethica, R., Chothia, C. and Gough, J. (2010) SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucl Acids Res. doi: 10.1093/nar/gkq1130. PDF
- Pethica R , Gough J (2012) - Evolutionarily Consistent Families in SCOP: Sequence, Structure and Function. BMC Structural Biology - in press