1. Welcome to Introduction to Bioinformatics The project

2. Go to the course’s main page and click either the Calendar or the List of Topics How to find your group

3. If the calendar, find a Genome Analysis link and click it.

4. How to find your group If the List of Topics, click Genome Analysis.

5. Once there, scroll down… How to find your group

6. …until you reach links to the Phage Annotation Groups and the Phage Analysis Groups Actually, they’re the same thing. Click either one.

7. How to find your group The usual window will pop up asking for the usual user name and password

8. How to find your group Darrell Britt Jay Gandhi Shirmeen Khan Sarah Siegfried Raiha Tahir Bunty Talati Eleni Galanopoulos Ryan Loviza Sara Oh Nick Santolla Ganesh Sosale Andrew Bengier Cynthia Faleti Lamis Farah Sheila Kapyur Viet Nguyen Kahley Stanco Darrell Britt Jay Gandhi Shirmeen Khan Sarah Siegfried Raiha Tahir Bunty Talati Andrew Cynthia Fi Lamis Farah Sheila Kapyur Viet Nguyen Kahley Sta Andrew Be Cynthia Fa Lamis Farah Sheila Kapyur Viet Nguye Kahley Stan Darrell Britt Jay Gandhi Shirmeen Khan Sarah Siegfried Raiha Tahir Bunty Talati Ben Koppenhaver Jay Gandhi Shirmeen Sarah Siegfried Raiha Tahir Darrell Siegfried Shirmeen Koppe Vishaka K Ravishankar Raiha Tahir Vishaka Ravishankar Bunty Talati Andrew Cynthia Fi Lamis Farah Sheila Kapyur Viet Nguyen Kahley Darrell Siegfrie Shirmeen K Vishaka K Ra Raiha Tahir Vishaka Ravis Bunty Talati Andrew Cynthia Fi Lamis Farah Sheila Kapyur Viet Nguyen Kahley Clicking an individual name will elicit that person’s e-mail address. Clicking the group name will elicit the e-mail addresses of everyone in the group.

9. How to find your group Darrell Britt Jay Gandhi Shirmeen Khan Sarah Siegfried Raiha Tahir Bunty Talati Eleni Galanopoulos Ryan Loviza Sara Oh Nick Santolla Ganesh Sosale Andrew Bengier Cynthia Faleti Lamis Farah Sheila Kapyur Viet Nguyen Kahley Stanco Darrell Britt Jay Gandhi Shirmeen Khan Sarah Siegfried Raiha Tahir Bunty Talati Andrew Cynthia Fi Lamis Farah Sheila Kapyur Viet Nguyen Kahley Sta Andrew Be Cynthia Fa Lamis Farah Sheila Kapyur Viet Nguye Kahley Stan Darrell Britt Jay Gandhi Shirmeen Khan Sarah Siegfried Raiha Tahir Bunty Talati Ben Koppenhaver Jay Gandhi Shirmeen Sarah Siegfried Raiha Tahir Darrell Siegfried Shirmeen Koppe Vishaka K Ravishankar Raiha Tahir Vishaka Ravishankar Bunty Talati Andrew Cynthia Fi Lamis Farah Sheila Kapyur Viet Nguyen Kahley Darrell Siegfrie Shirmeen K Vishaka K Ra Raiha Tahir Vishaka Ravis Bunty Talati Andrew Cynthia Fi Lamis Farah Sheila Kapyur Viet Nguyen Kahley Note the main time next to your group name. Starting the week of April 4, I will meet with each groups at the specified time (at a place to be named later). All of you are available at that time, according to the schedule you provided. The alternate time(s) may also be useful to you. No one in your group vetoed those times.

10. How to find your group Darrell Britt Jay Gandhi Shirmeen Khan Sarah Siegfried Raiha Tahir Bunty Talati Eleni Galanopoulos Ryan Loviza Sara Oh Nick Santolla Ganesh Sosale Andrew Bengier Cynthia Faleti Lamis Farah Sheila Kapyur Viet Nguyen Kahley Stanco Darrell Britt Jay Gandhi Shirmeen Khan Sarah Siegfried Raiha Tahir Bunty Talati Andrew Cynthia Fi Lamis Farah Sheila Kapyur Viet Nguyen Kahley Sta Andrew Be Cynthia Fa Lamis Farah Sheila Kapyur Viet Nguye Kahley Stan Darrell Britt Jay Gandhi Shirmeen Khan Sarah Siegfried Raiha Tahir Bunty Talati Ben Koppenhaver Jay Gandhi Shirmeen Sarah Siegfried Raiha Tahir Darrell Siegfried Shirmeen Koppe Vishaka K Ravishankar Raiha Tahir Vishaka Ravishankar Bunty Talati Andrew Cynthia Fi Lamis Farah Sheila Kapyur Viet Nguyen Kahley Darrell Siegfrie Shirmeen K Vishaka K Ra Raiha Tahir Vishaka Ravis Bunty Talati Andrew Cynthia Fi Lamis Farah Sheila Kapyur Viet Nguyen Kahley Clicking the name of the phage you will annotate will bring you to a page with possibly useful information about it.

11. Including the name of its purveyor.

12. How to annotate your phage We’ll talk about that in a future communication.

13. How to choose your research focus In this communication I’ll tell you about choices your group needs to make regarding a research focus.

14. How to choose your research focus You’ll choose from amongst six possible topics. I’ll introduce them, but you’ll find more in the appropriate Blackboard discussion forum. Good idea to pay it a visit.

15. How to choose your research focus Lysogeny Phage Bacterial chromosome Phage genome Prophage The Lysogeny Group will consider the protein and DNA binding sites needed by phage to achieve and maintain the lysogenic state. Remember lysogeny?

16. How to choose your research focus The Lysis Group will consider the protein and DNA binding sites needed by phage to break the host cell. Killing your host is not a decision to be made lightly. Do it too soon and you kill yourself. Too late, and you lose the race. Lysogeny Phage Bacterial chromosome Phage genome Prophage

17. How to choose your research focus The optimal time is when the the maximal number of phage particles have been manufactured. John Wertz, E. coli Genetic Stock Center, Yale U.

18. How to choose your research focus John Wertz, E. coli Genetic Stock Center, Yale U. Ry Young (1992) Microbiol Rev 56:430-481 Then the phage synthesizes enzymes that break the host’s cell wall to cause local bursts. What are these enzymes in your phage? It’s up to you to find out and tell the world about it.

19. How to choose your research focus The Sequence Bias Group will try to find measures of nonrandomness in the phage genomes. You’ll remember one example from a few days ago: different organisms have different preferences for the codons they use in protein synthesis…

20. How to choose your research focus Do the phages have the same codon preferences as their hosts? Some phages carry their own tRNAs. Does this influence codon preferences?

21. How to choose your research focus Do the phages have the same codon preferences as their hosts? Some phages carry their own tRNAs. Does this influence codon preferences?

22. How to choose your research focus The most common gene on earth encodes a protein that copies the gene that encodes it and propagates copies of it. Wouldn’t you know it?

23. How to choose your research focus The Mobile Element Group will attempt to identify such genes and the adjoining DNA sequences

24. How to choose your research focus A bacterium typically needs to replicate its genome (say 3 million nucleotides) in a leisurely several hours, before the next cell division. Phages are often under much greater time pressure. For example, in the case of phage T4: 300 copies x 170,000 nt per copy = 51 million nt in 30 minutes! With higher DNA synthesis requirements than the host, many phage encode their own DNA synthesis proteins. Mueser TC et al (2010) Virol J 7:359

25. How to choose your research focus Mueser TC et al (2010) Virol J 7:359 But it’s not all protein. ALL phage DNA need a beginning point, an origin of replication, that determines where DNA synthesis will begin. The DNA Replication Group will look for both phage-encoded DNA synthesis proteins and origins of DNA replication on phage genomes.

26. How to choose your research focus The Gene Regulation Group will look for proteins and protein-binding sites on phage genomes responsible for the regulation of the lytic process. We’ve seen already seen mechanisms that regulate expression of the phage repressor. There are many many other strategies.

27. How to choose your research focus All the groups will consider both genes (G) and DNA (D) features. G D G D G D G D G D G D

28. How to choose your research focus All the groups will consider evolutionary relationships amongst genes and proteins found in multiple related phages. G D G D G D G D G D G D

29. How to choose your research focus Your group should discuss amongst yourselves the virtues of each of the six choices. You should decide how to divide the effort required to make a rational decision. G D G D G D G D G D G D

30. How to choose your research focus Members of your group should visit the six research forums on the Blackboard Discussion page. You’ll find articles on each topic that may help you visualize how the project might play out.

31. How to choose your research focus When you have collectively made your decision, and no later than SUNDAY, March 4, midnight e-mail me the results of your deliberations, making sure that: - All members are copied - Numerical votes for each of the six choices are given. Choice 1: Choice 2: Choice 3: Choice 4: Choice 5: Choice 6: From: Designated group member Copy: All members E-mail 321000321000 If you are unable to reach a member of your group by Sunday afternoon, LET ME KNOW AT THAT TIME.

32. Viral Genomes Project Frederick Maverick Pari