Capstone Title

Techniques in the Characterization and Annotation of Hypothetical Functional and Regulatory Genes in Marine Microbial Genomes

Defense Date


Document Type


Degree Name

M.S. Biological Sciences

First Advisor

Jose V. Lopez

Second Advisor

Julie Torruellas Garcia


In this capstone, I describe various state-of-the-art tools in detail to “annotate” conserved hypothetical genes in whole genome sequences. Genetic annotation refers to the designation of function to biological sequences. This approach can be either experimental or bioinformatics based, the latter starting with identification, followed by structural and functional analyses using the RAST server, GLIMMER, and the SEED and KEGG databases. Eventually, gene expression studies should be carried out to experimentally test for gene function in a biochemical pathway and examples of this will be described. Bacterial operonic structure lends clues to gene function based on the surrounding genes if they are known, shows a putative biochemical function for a target gene of interest, and identifies regulator or operator sequences. First, identification by the GLIMMER system uses a computational gene finder to find genes using algorithms and models that rely on probability. Structural genomics approaches, such as protein production and crystallization, can then be carried out to give clues into biological function. The RAST server similarly creates metabolic networks and determines the roll of a gene in a subsystem. Functional genomics then generates functional linkage maps and 3D structures and links proteins that have a similar function called Rosetta-Stone proteins. Lastly, gene expression, explained by a seven-category model, helps to assign 5 function in addition to either a microarray or a gene knockout experiment where function is assessed before and after mutagenesis or gene fusions. Using all of these tools collectively aids in deducing function in hypothetical genes. This capstone report will document a number of case studies where functional identity has been determined by the above approaches.

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