EPWS 451/ BCHE 451/ MOLB 550

Lecture 2 Web Exercises and Projects Jan 21, 1998
craig@taipan.nmsu.edu
plammers@nmsu.edu

Important URLs for this lesson:

Genome Sequence Access:

http://www.ncbi.nlm.nih.gov/
http://pedant.mips.biochem.mpg.de/frishman/pedant.html
http://www.tigr.org/

NBIF Home Page:

http://www.nbif.org/


Published Complete Genomes

Organism Organization Citation

Haemophilus influenzae Rd	TIGR	Fleischmann et. al., Science 269:496-512 (1995)
Mycoplasma genitalium	TIGR	Fraser et. al., Science 270:397-403 (1995)
Methanococcus jannaschii	TIGR	Bult et. al., Science 273:1058-1073 (1996)
Synechocystis sp. PCC 6803	Kazusa DNA Research Inst.	Kaneko et. al., DNA Res. 3: 109-136 (1996)
Mycoplasma pneumoniae	Univ. of Heidelberg	Himmelreich et. al., Nuc. Acid Res. 24:4420-4449 (1996)
Saccharomyces cerevisiae	International Consortium EC, NHGRI, WelcomeTrust, McGill U., RIKEN	Goffeau et. al., Nature 387 (Suppl.) 5-105 (1997)
Helicobacter pylori	TIGR	Tomb et. al., Nature388:539-547 (1997)
Escherichia coli	University of Wisconsin NHGRI	Blattner et. al., Science 277:1453-1474 (1997)
Methanobacterium thermoautotrophicum	Genome Therapeutics & Ohio State Univ.	Smith et.al., J. Bacteriology,179:7135-7155 (1997)
Bacillus subtilis	International Consortium	Kunst et.al., Nature390: 249-256 (1997)
Archaeoglobus fulgidus	TIGR	Klenk et al.,Nature 390:364-370 (1997)
Borrelia burgdorferi	TIGR	Fraser et al., Nature, 390: 580-586 (1997)

Exercise 1.

• Go to the NCBI site.
• Open the Entrez page.
• Read the Entrez Help file, andd read about the five Entrez Databases.
• Explore each of the five data bases, then write a short paragraph describing the features of each database
• Read the BLAST help file (found on the BLAST page).

Exercise 2.

• Go to the NCBI site and find a " gene of interest" using any method you choose.
• Document the process by which you found your gene.
• Retrieve the Genbank file for your gene and print the header information only, NOT the DNA or derived amino acid sequences. How will you do this? If you don't know, ask.
• Highlight and "copy" the amino acid sequence of your gene of interest.
• Open the BLAST feature at NCBI and run a BLASTP and a TBLASTN search with your derived amino acid sequence as a query string.
• Compare the output by looking at the top 15 "hits". Note any differences.Print the best alignment produced by the BLAST server. (NOT the whole output, just the alignment).
• Repeat the procedure trying Gapped BLAST and note any differences between the alignments.
• Print the best GAPPED BLAST aligment below the first one.

Exercise 3.

• Go to the NBIF site
• Explore the Research Tools and Databases section of the site with special emphasis on the Databases section.
• Write down suggestions for improvement of the site with respect to: organization, content (additions, deletions).
• How easy is it to find information you are looking for there?

Exercise 4.

• Go to the Pedant site.Find a new gene of interest from one an organism of interest at that site.
• Pick a gene of interest for which a 3D structure is available. (Hint: there is a way to display this info for each organism.)
• Find out as much as you can about the product of your gene of interest on the Pedant site.
• Write a paragraph about your impressions of this site.

Exercise 5.

• Go to the TIGR site.
• Find the answer to the following question: How many ongoing whole genome sequencing projects are there?
• Write the answer down on your report.

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