Bio1AL_Fa09_lab7_manual - Bioinformatics and NCBI Version...

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Bioinformatics and NCBI Version 3.0 Jacob A. Mayfield, Meara Davies, John V. Gahagan, Jane O, Elizabeth Boydston, Nick Pleskac, and Jasper Rine November 14 th , 2008 Jacob Mayfield Jasper Rine University of California, Berkeley 176 Stanley Hall # 3220 Berkeley, CA 94720-3220 We gratefully acknowledge the contributions of Mark Andre, Rachel Doran, Atoosa Firouzian, Sarah Mogri, and Michael Meighan in developing and testing this module. We thank the Howard Hughes Medical Institute for financial support (2006 HHMI Professors Award number 52005727 to JR).
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1 Bioinformatics and NCBI INTRODUCTION Complete genomes sequences are available for over 500 different organisms and 2500 more genome projects are in progress. Additionally, the genome sequence of individuals or strains within a species are becoming available, changing the way we study genetic disease, trait variation and evolution. The direct product of all these genome projects is a tremendous amount of data in the form of nucleotide sequences. Access to these resources has revolutionized the way biologists operate: most modern laboratories have more computers than centrifuges. The purpose of this lab is to teach you to use some of the bioinformatics tools freely available to the scientific community, and in the process, to reinforce the concepts of the central dogma of molecular biology. You have probably heard DNA referred to as the blueprint of life. While most people can find the kitchen on a blueprint, an architect can find the weight-bearing beams and estimate the stability during an earthquake. Similarly, you might guess that a string of G’s, A’s, T’s, and C’s is DNA, but identifying the part of the sequence translated into protein, or the function of the gene, requires training. All of these tools are readily available online from NCBI, the N ational C enter for B iotechnology I nformation, and other free public resources. Many human genetic diseases are caused by one altered base pair among the three billion in the human genome. But one base pair in every few hundred already varies between any two individuals in the human population without causing a defect. Add the fact that most genetic diseases are the composite of several genes each contributing to the disease state, and the successes of scientists doing genetic disease research seem even more heroic. To better understand DNA sequence variation, genetic disease and the genetic code, we will focus on a series of human genes that have been implicated in a variety of disease states. We will use bioinformatics tools to go from a small amount of information to a working knowledge of DNA and protein sequences. Best of all, you will be learning to use resources you will need if you continue in the biological sciences. References:
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Bio1AL_Fa09_lab7_manual - Bioinformatics and NCBI Version...

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