PowerPoint Presentation - Introduction to Bioinformatics - Ccsf

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2 Οκτ 2013 (πριν από 3 χρόνια και 11 μήνες)

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Influenza

The Blame Game

The greatly feared pandemic flu virus has finally
broken out. Millions are sick and thousands have
already died. It is almost impossible for the Centers
for Disease Control (CDC) to keep track of the new
cases reported each day. Contrary to everyone's
expectations, the first reported cases appeared in
San Francisco and not in Asia or Eastern Europe.
From an anonymous source the New York Times is
reporting that there was mishandling of the recently
reconstituted and extremely dangerous 1918
influenza virus at several labs. Apparently, there was
unauthorized shipping of the virus to a Biosafety
Level 3 (BSL
-
3) lab at UC San Francisco and it …


The Blame Game

appears that the package might have been damaged
en route to the lab or potentially mishandled onsite at
UCSF. In immediate reaction to the newspaper's
report all related parties at UCSF have been arrested
for the illegal dissemination of a biological agent to
the public. Several of the arrested parties are
researchers without US citizenship (but with
appropriate visas) and some members of congress
are calling for immediate deportation or even
reclassification of their status to 'Enemy Combatants'
and trying them as terrorists. In other related news,
the virus strain from San Francisco has been fully
sequenced and, just today, released to the public.

PBS video


http://www.pbs.org/wgbh/nova/body/1918
-
flu.html



Influenza Virus (flu)


Small genome

8 RNA molecules

Antigenic glycoproteins


16 Hemagglutinins:

Attachement to host



9 Neuraminidases: Passage
through mucin, budding



-
E.g., H1N1

Influenza A, B, and C


A: the one that can cause pandemics, broad host
range (humans, birds, swine, horses…)


B: infects only seals and humans, ~ 1/3 of all
influenza cases in US


C: infects humans and swine, causes only mild
infections


Influenza Virus (flu)


Sequencing

Reverse
Transcriptase


DNA


Sequencing


Genomic Nucleotide
Sequence


Influenza Pandemics


1918 Flu


Killed from 50
-
100 Mil. people worldwide


Considered to be one of the most deadly pandemics


Killed many of the young and healthy


Influenza A, Type H1N1


Thought to have derived from Avian Influenza


Recently reconstituted from recovered human samples


Considerable ethical debate

Avian Influenza


Fear of pandemic


High mortality rate (including young and healthy)


Current concern is Influenza A, Type H5N1


Limited human
-
human transmission (2 cases as of
2009) in avian flu

Confirmed cases



Swine virus, the fear of viral
reassortment




HHMI animation





Post
-
pandemic stage of swine flu



Antiviral drugs


Amantadine +
Rimantadine


inhibit one of the matrix
proteins and thus passage
into the cytosol. By 2008
-
2009 season, virtually all
H3N2 were resistant.


.



Kimball’s Biology Pages

Antiviral drugs


Relenza and Tamiflu

block neuraminidase and
thus inhibit the attachment
of virions. By 2008
-
2009, all
H1N1 strains circulating in
the US were resistant.



.



Kimball’s Biology Pages

Introduction to
Bioinformatics

Alexandra M Schnoes

Univ. California San Francisco

Alexandra.Schnoes@ucsf.edu

What is Bioinformatics?


Intersection of
Biology

and
Computers


Broad field


Often means different things to different people



Personal Definition:


The utilization of computation for biological
investigation and discovery

the process by which you
unlock the biological world through the use of
computers.

What does one
do

in
Bioinformatics?




(a small sample)


dsafd


dsafd

?


Our Lab
: Understanding Protein (Enzyme) Function

What does one
do

in
Bioinformatics?




(a small sample)


Discover new drug targets

computational docking

Atreya, C. E. et al. J. Biol. Chem. 2003;278:14092
-
14100

Shoichet, B. K. Nature. 2004;432:862
-
865

What does one
do

in
Bioinformatics?




(a small sample)


Systems Biology

sbw.kgi.edu/


www.sbi.uni
-
rostock.de/ research.html

This lab: Nucleotide & Protein
Informatics



Sequence analysis


Finding similar sequences


Multiple sequence alignment


Phylogenetic analysis

Sequence

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Process of Evolution


Sequences change due to


Mutation


Insertion


Deletion

Use Evolutionary Principles to
Analyze Sequences


If sequence A and sequence B are similar


A and B evolutionarily related



If sequence A, B and C are all similar but A and B
are
more

similar than A and C and B and C.


A and B are more closely evolutionarily related to each
other than to C

Extremely Powerful Idea

1.
Start with
unknown

sequence


2.
Find what the
unknown

is similar to


3.
Use information about the
known

to make
predictions about the
unknown

How do you know when
sequences are similar?



Align two sequences together and score their similarity

TA
S
S
W
SY
I
V
E

TA
T
S
F
SY
L
V
G


Use substitution matrices to score the alignment

Substitution Matrices Give a
Score for Each Mutation


Many different matrices available


Blosum matrices standard in the field

Blosum 62 Scoring
matrix

http://www.carverlab.org/images/

Scoring: Add up the positional
Scores


Score of 30

TA
S
S
W
SY
I
V
E

TA
T
S
F
SY
L
V
G

TA
SSW
S
YIVE


TAT
S
FSYL
VG



Score of 1

Additional issues…


Gaps (insertions/deletions)


Have scoring penalties for opening and continuing a
gap

TASSWSYIVE

TA
S
S
W
SY
I
V
E

TATSFLVG

TA
T
S
F
--
L
V
G

How do we find similar
sequences?


Start at the National Center for Biotechnology
Information


http://www.ncbi.nlm.nih.gov/

How do we find similar
sequences?


Nucleotide Sequence Databases

How do we find similar
sequences?


Protein Sequence Databases

How do we find similar
sequences?


Similarity Search: BLAST


Basic Local Alignment Search Tool

BLAST is very quick but …


Only local alignments


Alignments aren’t great


Only pair
-
wise alignments

Want better alignments …


Multiple alignment


Multiple sequences


Better signal to noise


More Sequences = Better alignment


More accurate reflection of evolution


ClustalW


Commonly used


Easy to use


Visualize the Multiple Alignment


Use the Alignment to Calculate
Evolutionary Distances


See ‘how close’ sequences are to each other


Best way to tell what is ‘most similar’


Can calculate simple tree from clustalW

Taubenberger et al., Nature: 437, 889
-
893, 2005

Caveats!


In reality


Sequences (even
parts

of sequences) can evolve at
different rates


Don’t have a good understanding of sequence and
function


High sequence identity does not
always

mean the same
function


Getting good alignments and good trees can be very
hard

Bioinformatics: Sequence
Analysis

1.
Start with unknown sequence


2.
Find similar sequences


3.
Create alignment


4.
Create phylogenetic tree


5.
Use information about knowns to make
predictions about unknown