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Title: Computational analysis of proteomes from parasitic nematodes
Author: Wasmuth, James D.
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2006
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The focus of this thesis is the comparison of nematode proteomes. I describe my work to identify sequences and sequence features that have patterns of interest to nematode biology. Such patterns include proteins that are unique to a parasitic feeding strategy, and protein domains that have been lost in certain nematode lineages. This involved not only global comparisons of the proteomes, but also delineating the protein domain complement of each species. One vital step in the analysis is identifying credible coding regions within the error-prone EST sequences. Robust identification of the coding regions presents an opportunity to perform comparative analysis previously confined to those working with complete genomes. To achieve this, I built the translation pipeline prot4EST, a hierarchical collection of freely-available algorithms. The benchmarking showed that prot4EST produced coding region predictions that were better than its constituent algorithms. Exploring the effect of sequence composition of both the studied species and the program’s training sets improved the accuracy of prediction. A database of high quality protein translations for all nematodes studies was generated, called NemPep. This was accompanied by a collection of predicted domains (NemDom). The decoration of protein sequences with domain annotation is not trivial, especially given the incomplete nature of ESTs. It was necessary to explore domain model assignment to ensure the most accurate results. The rigorous analysis of these resources has revealed: (1) proteins specific to certain nematode lineages; (2) the level and potential effects of contamination in the original cDNA libraries; (3) the extent of protein loss and domain modification in the caenorhabditid lineage.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available