Bioinformatics methods for annotating genomes using proteomic data

Daniel Naguib, Gianluca Bioinformatics methods for annotating genomes using proteomic data. PhD thesis, University of Liverpool.

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Abstract

In recent years the number of genome sequencing projects has been exponentially increasing, leaving genome annotation dependent upon primarily automated tools. Recently, proteogenomics studies have attempted to bridge the gap between genomics and proteomics, by actively using proteomic data during the annotation stage. This project attempts to address some limitations in current bioinformatics approaches, such as the identification of N-terminal peptides and those spanning across exons – so called intron-spanning peptides (ISPs). Additionally it presents approaches for determining the quality of gene models. The results provide insights on the N-terminus of proteins (identification strategies, modifications), quality assessment on available gene annotation and performance of gene finders. A new method has also been developed for the identification of ISPs and, although this technique remains challenging, provides a framework in which future developments can be made.

Item Type:	Thesis (PhD)
Additional Information:	Date: 2014-09 (completed)
Depositing User:	Symplectic Admin
Date Deposited:	10 Feb 2015 09:47
Last Modified:	17 Dec 2022 01:30
DOI:	10.17638/02003079
URI:	https://livrepository.liverpool.ac.uk/id/eprint/2003079