welcome to introduction to bioinformatics the project

Welcome toIntroduction to Bioinformatics

The project

Go to the course’s main page and click either the Calendar

or the List of Topics

How to find your group


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


If the List of Topics, click Genome Analysis.

Once there, scroll down…


How to find your group…until you reach links to the Phage Annotation Groups and

the Phage Analysis Groups

Actually, they’re the same thing.

Click either one.


The usual window will pop up asking for the usual

user name and password


Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati

Eleni GalanopoulosRyan LovizaSara OhNick SantollaGanesh Sosale


Andrew BengierCynthia FaletiLamis FarahSheila KapyurViet NguyenKahley Stanco




Andrew Cynthia FiLamis FarahSheila KapyurViet NguyenKahley Sta

Andrew BeCynthia FaLamis FarahSheila KapyurViet NguyeKahley Stan


Ben KoppenhaverJay GandhiShirmeen Sarah SiegfriedRaiha Tahir

Darrell SiegfriedShirmeen KoppeVishaka K RavishankarRaiha TahirVishaka RavishankarBunty Talati

Andrew Cynthia FiLamis FarahSheila KapyurViet NguyenKahley

Darrell SiegfrieShirmeen KVishaka K RaRaiha TahirVishaka RavisBunty Talati


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.

















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.

















Clicking the name of the phage you will annotate will bring you to a page with possibly useful information about it.

Including the name of its purveyor.

How to annotate your phage

We’ll talk about that in a future communication.

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

How to choose your research focusYou’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.

How to choose your research focus

Lysogeny

Phage

Bacterial chromosomePhage 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?


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 chromosomePhage genome

Prophage


The optimal time is when the the maximal number of phage particles have been manufactured.

John Wertz, E. coli Genetic Stock Center, Yale U.


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.


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…


Do the phages have the same codon preferences as their hosts?

Some phages carry their own tRNAs. Does this influence codon preferences?


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?


The Mobile Element Group will attempt to identify such genes and the adjoining DNA sequences

How to choose your research focusA 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


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.

How to choose your research focusThe 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.


All the groups will consider both genes (G) and DNA (D)

features.

GD

GD

GD

GD

GD

GD


All the groups will consider evolutionary relationships amongst

genes and proteins found in multiple related phages.

GD

GD

GD

GD

GD

GD


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.

GD

GD

GD

GD

GD

GD


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.


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 memberCopy: All members

E-mail

321000

If you are unable to reach a member of your group

by Sunday afternoon,

LET ME KNOW AT THAT TIME.

Viral Genomes Project

Frederick

Maverick

Pari

welcome to introduction to bioinformatics the project

Documents

phage analysis groupsactually

main time

genome analysis link

phage annotation groups

specified time

list of topicshow

email addresses

usual user