5: Introduction to databases
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The computer belongs on the benchtop in the modern biology lab, along with other essential equipment. A network of online databases provides researchers with quick access to information on genes, proteins, phenotypes, and publications. In this lab, you will collect information on a MET gene from a variety of databases.
At the end of this lab, students should be able to:
- explain how information is submitted to and processed by biological databases.
- use NCBI databases to obtain information about specific genes and the proteins encoded by those genes.
- describe the computational processes used by genome projects to decode DNA sequences and process the information for molecular databases.
- use the Saccharomyces Genome Database to obtain information about role(s) that specific proteins play in yeast metabolism and the phenotypic consequences of disrupting the protein’s function.
Biomedical research has been transformed in the past 25 years by rapid advances in DNA sequencing technologies, robotics and computing capacity. These advances have ushered in an era of high throughput science, which is generating a huge amount of information about biological systems. This information explosion has spurred the development of bioinformatics, an interdisciplinary field that requires skills in mathematics, computer science and biology. Bioinformaticians develop computational tools for collecting, organizing and analyzing a wide variety of biological data that are stored in a variety of searchable databases. Today’s biologist needs to be familiar with online databases and to be proficient at searching databases for information.
Your team has been given three S. cerevisiae strains, each of which is missing a MET gene. In the next few labs, you will determine which MET gene is deleted in each strain. To identify the strains, you will need information about the MET gene sequences that have been disrupted in the mutant strains. You will also need information about the role that each of the encoded proteins plays in methionine synthesis. In this lab, you will search for that gene-specific information in several online databases. Each member of the group should research a different one of the threeMET genes. As you progress through this lab, you may feel like you are going in circles at times, because you are! The records in databases are extensively hyperlinked to one another, so you will often find the same record via multiple paths. As you work through this chapter, we recommend that you record your search results directly into this lab manual.