Chapter 2 Web Exploration: Finding and Manipulating Genetic Data

Preparation:

Form a new group that includes at least one student with a CS background and at least one student with a Biology background. In forming your group you should not include anyone you worked with on a prior lab or homework assignment.

Any student may be at the keyboard.

Please read through the whole lab before beginning.

Task:

Do Web Exploration 2.5.1, which appears on pages 25-29.

Warning:

As you may know, the default setting for the Web browser in the MathLAN is to disable Javascript on most sites. However, Javascript is necessary for the NCBI sites. Make sure to turn on scripts for any site that you visit.

Notes:

You will find that some of what you do in this lab is what you did in the Web Exploration for the previous chapter. At this point, some reinforcement is good.

You will not turn in anything for this lab. However, you should be prepared to answer the questions that appear on pages 27 and 29.

You will follow some detailed sets of instructions for finding things. You may want to take some notes on those instructions, so that you can use them more easily the next time.

We will also ask you to think about some more general issues. Here are a few other questions you might think about.

Did the exploration help you find better ways to look for DNA?
Does the FASTA file for HBB use the template sequence or the coding sequence? How do you know?
At one point, there were typos in the GenBank record. Are they still there?
What software can you use to compare sequences?
If you were writing the analysis code, what procedures would you want to write? (Or what procedures would you want your programmer to write?)

If you complete this lab early, you may want to begin the programming lab for Chapter 2.

History

Monday, 5 September 2011 [Samuel A. Rebelsky]

Created. (These short labs in the Course web provide a more convenient way to give students access.)
This version available at http://www.cs.grinnell.edu/~rebelsky/Courses/CS295/2011F/Labs/chap2-web.html.

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