Biotechnology/Bioinformatics Discovery!

 

Introduction to Bioinformatics

 

The following exercise is best accomplished by starting at our program web site
www.occc.edu/BBDiscovery and clicking on the Modules link and then clicking on
the Introduction to Bioinformatics link to access this exercise online.

 

Go to this site: http://wiki.bioinformatics.org/Bioinformatics_FAQ

 

I.       What is bioinformatics?

 

 

 

1. who is the author of this web page – his name and credentials (hint: go to end of page for the latter):

 

 

2. how does the author define bioinformatics:

 

 

 

3. what role did the Human Genome Project play in developing the field of bioinformatics:

 

 

 

 

4. what is the writer’s view of the prospects for a career in bioinformatics? (scroll down to the careers link)

 

 

 

5. what kinds of skills and knowledge does a person have to have to work in bioinformatics?

 

 

 

 

II.    More on Bioinformatics

To know more about what all those notations mean that are given on the results page of a
 BLAST search, there is an excellent tutorial to take you through the steps and terminology
of a BLAST search – go to the page titled “Blast for Beginners” located at 
http://www.digitalworldbiology.com/dwb/Tutorials/Entries/2009/1/26_BLAST_for_Beginners.html  Follow the green arrows
to complete the 12 slide tutorial.

As you work through this tutorial, you should be able to answer the following questions.

1.  What does BLAST stand for?

2.  The BLAST site is maintained by what agency?

3. How long is the first sequence that the tutorial pasted in the BLAST database box?

4.  How many sequences are in the database for comparison?

5. What organism is the source of the sequence?

6.  Note the blue letters (hyperlinks) that are given to the left of the sequence description. 
     In general, what are they used for?

 

 

7. What is the definition of the E value?
    Is a higher or lower E value better? _________  Why?

 

 

 

8.  In this same tutorial example, what % of the query matched exactly with the database?

 

9.   Using the tutorial page that lists the accession number at the top left of the screen
       find out:

(a)    the taxonomy of this organism (just list the first 3)

(b)   name the journal this sequence was first published in  and the year

(c)    the authors of the journal are?

 

III.  Try your hand at bioinformatics: "BLASTing through the Kingdoms of Life"

Here is a simple exercise in using a national database to identify a DNA sequence. It’s as easy as cutting and pasting!
** HINT: it works easier if you have 2 browser windows open at the same time **.

IV.  To Summarize – 

1.  Now that you have used a computer and the Internet to obtain identities of DNA
 sequences with relative ease, imagine doing this task – taking a DNA sequence
 and searching a database of sequences – without a computer.  In your own words,
 describe why bioinformatics is a part of today’s biology.

2.  For a description of the role of bioinformatics in the Human Genome Project,
     see www.accessexcellence.com/WN/SUA14/genome2.html. 
  To learn more about the Human Genome Project, use our BBDiscovery module located at
    www.occc.edu/bbdiscovery/documents/Modules/Human%20Genome%20Project%20Module.htm

Credits:  Geospiza, Austin Community College, ASM Instructional Library.