b'@mastersthesis{Schlicker2005,'b'\nTITLE = {A Global Approach to Comparative Genomics: Comparison of Functional Annotation over the Taxonomic Tree},\nAUTHOR = {Schlicker, Andreas},\nLANGUAGE = {eng},\nLOCALID = {Local-ID: C125673F004B2D7B-76B88A36B2C63828C12570EB004472E7-Schlicker2005},\nSCHOOL = {Universit{\\"a}t des Saarlandes},\nADDRESS = {Saarbr{\\"u}cken},\nYEAR = {2005},\nDATE = {2005},\nABSTRACT = {Genome sequencing projects produce large amounts of data that are stored in <br>sequence databases. Entries in these databases are annotated using the results <br>of different experiments and computational methods. These methods usually rely <br>on homology detection based on sequence similarity searches.<br>Gene Ontology (GO) provides a standard vocabulary of functional terms, and <br>allows a coherent annotation of gene products. These annotations can be used as <br>a basis for new methods that compare gene products on the basis of their <br>molecular function and biological role.<br>In this thesis, we present a new approach for integrating the species taxonomy, <br>protein family classifications and GO annotations. We implemented a database <br>and a client application,<br>GOTaxExplorer, that can be used to perform queries with a simplified language <br>and to process and visualize the results. It allows to compare different <br>taxonomic groups regarding the protein families or the protein functions <br>associated with the different genomes. We developed a method for comparing GO <br>annotations which includes a measure of functional similarity between gene <br>products. The method was able to find functional relationships even if the <br>proteins show no significant sequence similarity. We provide results for <br>different application scenarios, in particular for the identification of new <br>drug targets.},\n}\n'