INTRODUCTION
These exercises have been designed
to help teach students some of the basic tools of bioinformatics
data mining. At IU, they are used in conjunction with
introductory biochemistry courses C483 and C484, but they can be
easily incorporated into a variety of curricula or performed
independently. For the time being, the exercises focus primarily
on proteins rather than nucleic acid sequences. This omission is
only a practical issue regarding how much material can be
incorporated into one term of biochemistry. Eventually,
exploration of nucleic acid sequences will be added. At that
point, instructors will have to either provide additional time to
complete the exercise or select only a subset of the exercises
for use in any given term.
Instructions:
If this is your first time on this site, you may press
the blue button to be assigned an unknown peptide. Then complete
the registration form filling in the number of the unknown you
have been assigned. If you are part of a class that has
pre-registered for use of this site, enter your username in the
box provided and press the green submit button. If you are
returning to the site to complete additional projects that you
have already begun, you may enter either your username or the
unknown number to pick up where you left off. Once you have a
pair of peptides visible in the bottom window continue to
exercise one and follow the stepwise instructions through the
process of identifying your unknown protein. After completing
this exercise, the other exercises can be performed independently
and in any order. Several questions are available at the end of
each exercise to help you think about the output you obtained and
the process of finding that information. Try to spend 25% of your
effort obtaining the output and about 75% of your effort
analyzing and interpreting that material. It is important that
you learn to identify when the information provided by the
computer is accurate and when you are being misled due to an
error in the input or simply insufficient statistical
significance.
Known software compatibility issues (as of 08/09/02):
The flash program that assigns unknowns requires Flash Player 6.0 or
higher. Download Macromedia Flash Player at http://www.macromedia.com/downloads/.
The exercises have been developed using Netscape 4.7x and are fully functional on this browser. Intermittently, there have been reports of problems with IE 6.0, especially printing from sites with embedded CHIME figures.
Many of the sites used in these exercises require the CHIME plug-in module. Download CHIME at http://www.mdlchime.com/chime/.
Some of the sites require
Shockwave. Download Shockwave Player at link tohttp://sdc.shockwave.com/shockwave/download/frameset.fhtml.