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Senior Project - GeneACT


Web-based Bioinformatics Tool for Promoter Analysis and Experiment Design

Senior Project: 2003-2004
Genevieve Hudak, Yin (Phoenix) Kwan, Mai Sasaki, Stephen Smithwick and Jinhua Zhang

The main focus of the Xuedong Liu Laboratory in the Department of Chemistry and Biochemistry at the University of Colorado Boulder is to understand the mechanism(s) of signaling by the transforming growth factor beta (TGF-) in normal and cancer cells. TGF- is a multi-functional cytokine responsible for regulating growth and differentiation of a wide variety of cell types and tissues.

What biochemists need now are interactive computer databases and analytic programs to compare human DNA sequences with the sequences from other species. Since sequences that define a particular gene feature are conserved among different species, biochemists want to know if there are any yet unknown promoter binding sites in the conserved regions of multiple species. In other words, biochemists are trying to discover if there are short genetic sequences that promote the process of making proteins, and if so, where those are located.

The goal of the project is to help biochemists speed up their gene search process and to manage the massive amount of information produced during their studies. Furthermore, the biochemists' new findings will be beneficial to all mankind as it is applied to the medical industry.

The system provides a web site that can assist biochemists in the process of deciphering and analyzing the conserved sequences in the genomes. This web site provides high throughput comparative genome analysis, in which a user can search for binding sites in a huge set of genes in a relatively short period of time. One of the tools looks for conserved sequences between genomes of different species, such as human, mouse, and rat. The tool can display the gene sequence alignments graphically as well as textually. With the help of this tool, the scientists can gain access to the functional patterns in the human and mouse genomes more efficiently and can also facilitate the design of their experiments, such as the design of PCR primers.

PCR Primer Generator
PCR Primer Generator
Potential Binding Site Result
Potential Binding Site Result
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May 5, 2012 (14:07)