Download - Welcome to Introduction to Bioinformatics
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Welcome toIntroduction to Bioinformatics
The project
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Go to the course’s main page and click either the Calendar
or the List of Topics
How to find your group
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How to find your group
If the calendar, find a Genome Analysis link and click it.
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How to find your group
If the List of Topics, click Genome Analysis.
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Once there, scroll down…
How to find your group
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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.
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How to find your group
The usual window will pop up asking for the usual
user name and password
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How to find your group
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
Eleni GalanopoulosRyan LovizaSara OhNick SantollaGanesh Sosale
Eleni GalanopoulosRyan LovizaSara OhNick SantollaGanesh Sosale
Andrew BengierCynthia FaletiLamis FarahSheila KapyurViet NguyenKahley Stanco
Andrew BengierCynthia FaletiLamis FarahSheila KapyurViet NguyenKahley Stanco
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
Andrew Cynthia FiLamis FarahSheila KapyurViet NguyenKahley Sta
Andrew BeCynthia FaLamis FarahSheila KapyurViet NguyeKahley Stan
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
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
Andrew Cynthia FiLamis FarahSheila KapyurViet NguyenKahley
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.
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How to find your group
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
Eleni GalanopoulosRyan LovizaSara OhNick SantollaGanesh Sosale
Eleni GalanopoulosRyan LovizaSara OhNick SantollaGanesh Sosale
Andrew BengierCynthia FaletiLamis FarahSheila KapyurViet NguyenKahley Stanco
Andrew BengierCynthia FaletiLamis FarahSheila KapyurViet NguyenKahley Stanco
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
Andrew Cynthia FiLamis FarahSheila KapyurViet NguyenKahley Sta
Andrew BeCynthia FaLamis FarahSheila KapyurViet NguyeKahley Stan
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
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
Andrew Cynthia FiLamis FarahSheila KapyurViet NguyenKahley
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.
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How to find your group
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
Eleni GalanopoulosRyan LovizaSara OhNick SantollaGanesh Sosale
Eleni GalanopoulosRyan LovizaSara OhNick SantollaGanesh Sosale
Andrew BengierCynthia FaletiLamis FarahSheila KapyurViet NguyenKahley Stanco
Andrew BengierCynthia FaletiLamis FarahSheila KapyurViet NguyenKahley Stanco
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
Andrew Cynthia FiLamis FarahSheila KapyurViet NguyenKahley Sta
Andrew BeCynthia FaLamis FarahSheila KapyurViet NguyeKahley Stan
Darrell BrittJay GandhiShirmeen KhanSarah SiegfriedRaiha TahirBunty Talati
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
Andrew Cynthia FiLamis FarahSheila KapyurViet NguyenKahley
Clicking the name of the phage you will annotate will bring you to a page with possibly useful information about it.
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Including the name of its purveyor.
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How to annotate your phage
We’ll talk about that in a future communication.
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How to choose your research focusIn this communication I’ll tell you about choices your group needs to make regarding a research focus.
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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.
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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?
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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 chromosomePhage genome
Prophage
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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.
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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.
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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…
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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?
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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?
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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?
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How to choose your research focus
The Mobile Element Group will attempt to identify such genes and the adjoining DNA sequences
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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
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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.
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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.
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How to choose your research focus
All the groups will consider both genes (G) and DNA (D)
features.
GD
GD
GD
GD
GD
GD
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How to choose your research focus
All the groups will consider evolutionary relationships amongst
genes and proteins found in multiple related phages.
GD
GD
GD
GD
GD
GD
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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.
GD
GD
GD
GD
GD
GD
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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.
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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 memberCopy: All members
321000
If you are unable to reach a member of your group
by Sunday afternoon,
LET ME KNOW AT THAT TIME.
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Viral Genomes Project
Frederick
Maverick
Pari