Download Organization of Project

Introduction to Bioinformatics
Wednesday, 2 March 2011
Genome analysis
• Introduction to Wally and Batiatus
• Organization of research groups
• Hatfull et al (2008)
• Break up into research groups
This demonstration is best viewed as a slide show,
enabling you to simulate a session and make
changes
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Viral Genomes Project
Viral Genomes Project
Wally
Rachel Walstead
Batiatus
and
Danielle Renner
Introduction to Bioinformatics
Wednesday, 2 March 2011
Genome analysis
• Introduction to Wally and Batiatus
• Organization of research groups
• Hatfull et al (2008)
• Break up into research groups
Organization of Project
The organization of the project can be found
on the Genome Analysis module page
Organization of Project
The page has the same sort of things that you’ve
become used to in module pages
– a place to find notes, problem sets, etc
But in addition to all that (scroll down)…
Organization
ofgroups.
Project
…there’s a section on analysis
It’s divided into two parts:
• Annotation of our two phage, Wally and Batiatus
• Analysis of different aspects of bacteriophage
genomes
First, phage annotation. Let me give an example, using BioBIKE.
For phage annotation, it’s essential that
you log into PhAnToMe/BioBIKE.
If you’re using a wireless connection and
find you’re blocked, try the alternate link.
Organization of Project
Suppose you want to annotate your favorite genes.
Go to the ANNOTATION menu and bring
down a VIEW-GENE box
Organization of Project
Enter the name of the gene by clicking
the gene-or-protein box…
Organization of Project
… which gene?
I’ll choose one you’re familiar with.
(PhiLC3? Remember that one?)
Execute the function.
Organization of Project
This brings you to the gene’s annotation page.
If you want to know something about the
gene’s physiological role or regulation,
this is the place…
…Hmmm. 0? There doesn’t seem to be
anything here. This is where you come in.
But for now, keep on going. Scroll down.
is a genetic map of the region surrounding
OrganizationThistheof
Project
gene,
both in PhiLC3 and some other
phage. Potentially very useful!
Mouse over the red gene marked 1.
It tells you that the gene is currently
annotated as the phage repressor.
(I hope there’s good evidence
for that assertion!)
Move the cursor a couple
of genes to the left
Feature
ID
Function
Contig
Start
Stop
Size
Set
fig|12390.1.peg.3
Phage repressor
NC_005822
2781
1921
861 nt, 287 aa
1
It says it’s a transcriptional regulator…
No doubt! But Blatny et al had
a lot more to say than that!
You could make significant improvements
in this annotation, but for now scroll back up.
Feature
ID
Function
Contig
Start
Stop
Size
Set
fig|12390.1.peg.5
Transcriptional regulator
NC_005822
3222
3452
231 nt, 77 aa
16
Organization of Project
You probably had a difficult time finding
the gene during the exam, because the name
Orf286 used by Blatny et al was unknown to
BioBIKE. You could make things easier on the
next person by adding that name to the aliases.
To change the aliases,
just click on the yellow box.
Organization of Project
Clicking the box enables you to change its
contents. Type in Orf286
Organization of Project
But as you may have noticed (and if not,
you will!), there are all sorts of crazy things
in annotations. Every change you made
should have a reason.
Click the Justification box to supply a reason.
Organization of Project
That’s fair. The name was used in a published
article. But you can’t expect someone else to
know what “Blatny et al (2003)” means. You
need to provide the full reference.
Don’t remember it? Click the PubMed button.
Now, with a few choice terms,
you can find the article.
To bring the reference into BioBIKE,
you should be able to just copy
the PMID (PubMed ID)…
…but that trick isn’t working yet. So for
now, get the URL of the article, either
by right clicking the article and choosing
Copy Link Location, or clicking the article…
…and just copying the URL
directly from the browser
Organization of Project
Paste the URL into the
Justification Link box…
… and click SAVE
The change you made has been incorporated
into the PhAnToMe data base.
If you mouse over the Justification icon…
Organization of Project
…you’ll see that your change worked.
It is now visible to the world.
Move the cursor a bit to the right,
over the History icon…
…and you’ll see the author of the
current version of the alias field,
also visible to the world.
If someone disagrees with the change
(or wants to find out more about the reasons),
clicking on the name will generate an
e-mail to the author.
This is how you’ll enter information
about the genes you annotate.
Your primary responsibility will be towards the
genes of either Wally or Batiatus, but you (and
anyone else in the world) are free to annotate
any gene you know about.
Organization of Project
Groups 1 through 4 are primarily
responsible for Wally, and Groups 5 and 6
are primarily responsible for Batiatus.
More on this in a moment, but for now, let’s
consider the second part: Analysis.
Scroll down to put all the analysis
groups on the screen.
Organization of Project
The Lysogeny Group will consider the protein and DNA binding sites needed by
phage to achieve and maintain the lysogenic state. Remember lysogeny?
Phage
Lysogeny
Prophage
Phage genome
Bacterial chromosome
Organization of Project
Note that this group (like all of them) comes with a couple of focus questions
and a reference (usually a review article) that might help you get started.
Phage
Lysogeny
Prophage
Phage genome
Bacterial chromosome
Organization of Project
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.
Phage
Lysogeny
Prophage
Phage genome
Bacterial chromosome
Organization of Project
The optimal time is when the the maximal number
of phage particles have been manufactured.
John Wertz, E. coli Genetic Stock Center, Yale U.
Organization of Project
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.
Ry Young (1992) Microbiol Rev 56:430-481
John Wertz, E. coli Genetic Stock Center, Yale U.
Organization of Project
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…
Organization of Project
Do the phages have the same codon preferences as their hosts?
Some phages carry their own tRNAs.
Does this influence codon preferences?
Organization of Project
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?
Organization of Project
The Mobile Element Group will attempt to identify
such genes and the adjoining DNA sequences
Organization of Project
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
Organization of Project
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.
Mueser TC et al (2010)
Virol J 7:359
Organization of Project
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.
Organization of Project
G
D
G
D
D
G
G
D
G
D
G
D
All the groups will consider
both genes (G) and DNA (D)
features.
Organization of Project
All groups will consider how their genes cluster and how
the clustering relates to the overall clustering of phage genomes…
Organization of Project
…and how the clustering might be viewed as an evolutionary tree.
All of this takes both analysis of your phage sequences and an appreciation
of the analyses others have done before you. How to get that appreciation?
You and others in your group
will need to look at lots of articles.
But lots starts with the first one. In the
next two weeks, in consultation with
your group, you should identify a useful
article, one that broadens the knowledge
of your group on your topic.
Organization of Project
To help you make sense out of articles,
you’ll have the opportunity to write a
summary of that article…
What’s a summary? Click on the link…
Organization of Project
Key elements:
• Choose a research article (not a review).
• Focus on just one experiment.
• Understand that experiment and its
result to the bone.
• Add your knowledge to PhAnToMe.
Organization of Project
I hope you now see that there will need
to be a lot of interaction with your
group and focus on your topic.
But what is your group?
What is your topic?
To answer the first, click Analysis Groups.
Organization of Project
The groups were chosen
according to the schedules
you provided, to make sure
that there was at least one
time you all could meet.
You can change that time
(or supplement it), so long
as there is one time that
does not conflict with the
times of others (so that
I can attend the meeting).
Organization of Project
Each group has been
assigned part of a phage
to annotate. For example,
Group 1 has all the genes
that overlap with the
first 40,000 nucleotides
of Wally.
That group will find all
genes in that region,
determine the functions of
the proteins, and put the
information into
PhAnTome. (We’ll talk
more about this)
Groups can distribute
nucleotides to its members
however they like.
Organization of Project
But which group gets which Analysis Groups?
You’ll get details in a forthcoming email, but in brief…
Organization of Project
• Each group will submit one set of choices.
The group must first arrive at a consensus.
• Each group will have 10 votes, which it
can distribute any way it likes.
• An algorithm will take the six group votes
and use them to maximize happiness
For example…
Organization of Project
Your group might cast 7 votes for Gene
Regulation, and 3 for Mobile Elements. If
your group has the highest number of votes
for Gene Regulation, you’ll probably get it.
But if you cast all of your 10 votes for Gene
Regulation, and another group has done the
same, then that group might get Gene
Regulation, and you will be probably be
given whatever’s left over, probably an
analysis group that attracted little interest
from other groups.
(Not sure how best to achieve your ends?
You might try to simulate the game.)
Introduction to Bioinformatics
Wednesday, 2 March 2011
Genome analysis
• Introduction to Wally and Batiatus
• Organization of research groups
• Hatfull et al (2008)
• Break up into research groups
Hatfull et al (2008): Protein families
Hatfull Graham F, Cresawn Steven G, Hendrix Roger W (2008) Res Microbiol 159:332-339
Introduction to Bioinformatics
Wednesday, 2 March 2011
Genome analysis
• Introduction to Wally and Batiatus
• Organization of research groups
• Hatfull et al (2008)
• Break up into research groups
Organization of Project
Analysis Groups (Geography)
Group 4
Group 3
Group 2
Group 5
Group 1
Group 6
FRONT