How antigens are processed so that they can be presented by MHC
molecules to T cells?
Cytotoxic T-cells/Tc cells
-2 microglobulin
HelperT-cells/Th cells
2 domain
Cytosolic pathway / Endogenous pathway/MHC I
Proteasome
Large multifunctional protease comple

Outline
www.
1. Introduction to sequence alignment
2. pair wise sequence alignment
a) The Dot Matrix
b) Scoring Matrices
c) Gap Penalties
d) Dynamic Programming
.uni-rostock.de
Introduction to sequence alignment
www.
.uni-rostock.de
Sequence Alignment is

Accession numbers are labels
for sequences
NCBI includes databases (such as GenBank) that contain
information on DNA, RNA, or protein sequences.
You may want to acquire information beginning with a
query such as the name of a protein of interest, or the
r

Outline of todays lecture
Summary of key points about pairwise alignment
Introduction to BLAST: practical guide to database searching
The BLAST algorithm
BLAST search strategies
Text Books:
1. BIOINFORMATICS (sequence, structure and
databanks) by
D

Th.H.M. Noij and I. Bobeldijk
Kiwa Water Research, PO Box 1072, 3430 BB Nieuwegein, The Netherlands (E-mail: [email protected])
Abstract Two novel water quality monitoring concepts were developed: the HPLC-fingerprint for the
monitoring of yet unidentifie

11. ENERGY CONSERVATION
Topics
Energy Conservation
Energy Saving by Energy Efficient Motor
Energy Saving by CFL for Street Lighting
Energy Saving in Agricultural Pump
Energy Conservation in Buildings
Energy Saving at home
WHAT IS ENERGY CONSERVATION

3. LIQUID FUELS
Topics:
Petroleum or Crude Oil
Petroleum Refining Process
World and Indian Oil Scenario
Indian Oil Economics
Liquid fuel in transportation sector
Other liquid fuels
Biodiesel, Ethanol and Methanol
PETROLEUM / CRUDE OIL
A fossil fue

Docking: Structure Analysis And Docking Of
Ring Hydroxylating Enzyme With Its
Substrate From
Different Species
Homology
Modeling?
NMR ?
X-ray ?
Structural Genomics project
Aim to solve the structure of all proteins: this
is too much work experimentally!

Advanced BLAST Searching
Position specific iterated BLAST:
PSI-BLAST
The purpose of PSI-BLAST is to look deeper
into the database for matches to your query
protein sequence by employing a scoring
matrix that is customized to your query.
Page 137
PSI-BLAST

Major Histocompatibility Complex
(MHC)
&
Antigen processing and
presentation
MHC
Tightly linked cluster of genes
Discovered to play a role in transplant rejection
Role in intercellular recognition
In discrimination between self and non-self.
MHC complex

Outline of todays lecture
Summary of key points about pairwise alignment
Introduction to BLAST: practical guide to database searching
The BLAST algorithm
BLAST search strategies
Text Books:
1. BIOINFORMATICS (sequence, structure and
databanks) by
D

1
Magnetic Materials
&
Superconductivity
Definition of a Magnetic Dipole Moment
A magnetic moment
2
3
Magnetic Dipole Moment
m IAu n
Magnetic moment
Current
Unit vector normal to the
surface
Area circled by current
Magnetic moment experiences a torque in

Th.H.M. Noij and I. Bobeldijk
Kiwa Water Research, PO Box 1072, 3430 BB Nieuwegein, The Netherlands (E-mail: [email protected])
Abstract Two novel water quality monitoring concepts were developed: the HPLC-fingerprint for the
monitoring of yet unidentifie

Textbooks
Several bioinformatics texts are available:
Baxevanis and Ouellette
David Mount
Durbin et al.
Web sites
The course website is:
http:/pevsnerlab.kennedykrieger.org/
bioinfo_course.htm
This site contains the powerpoints for each lecture.
The textb

Protein databases and structures
Course Outline
Lectur Subjects
e
1
Introduction, major useful public
databases and genome browsers
2
Homologue finding, sequence
alignment, multiple alignment,
phylogeny trees
3
Protein databases: sequence and
structure, m

4. GASEOUS FUELS
Topics:
Compressed Natural Gas (CNG)
Liquefied Natural Gas (LNG)
Liquefied Petroleum Gas (LPG)
WHY GASEOUS FUELS ?
Huge reserves available
Clean combustion and higher
combustion efficiency
End user convenience (Kerosene vs LPG)
Tra

9. BIOMASS ENERGY
Topics:
Biomass types,
Characterization,
Conversion routes,
Bio chemical
BIOMASS
Biomass is biological/organic material derived from living,
or recently living organisms. (The term is equally applicable
to both animal and vegetable

Chapter 6
Limits of Functions
In this chapter, we define limits of functions and describe their properties.
6.1. Limits
We begin with the !- definition of the limit of a function.
Definition 6.1. Let f : A R, where A R, and suppose that c R is an
accumula

Chapter 2
Numbers
God made the natural numbers; all else is the work of man. (Leopold
Kronecker, quoted by Weber, 1893)
God created the integers and the rest is the work of man. This maxim
spoken by the algebraist Kronecker reveals more about his past as

Chapter 9
Sequences and Series of
Functions
In this chapter, we define and study the convergence of sequences and series of
functions. There are many different ways to define the convergence of a sequence
of functions, and different definitions lead to in

Chapter 10
Power Series
In discussing power series it is good to recall a nursery rhyme:
There was a little girl
Who had a little curl
Right in the middle of her forehead
When she was good
She was very, very good
But when she was bad
She was horrid.
(Robe

Chapter 8
Differentiable Functions
A differentiable function is a function that can be approximated locally by a linear
function.
8.1. The derivative
Definition 8.1. Suppose that f : (a, b) R and a < c < b. Then f is differentiable
at c with derivative f

Chapter 4
Series
Divergent series are the devil, and it is a shame to base on them
any demonstration whatsoever. (Niels Henrik Abel, 1826)
This series is divergent, therefore we may be able to do something
with it. (Oliver Heaviside, quoted by Kline)
In t

Chapter 1
Sets and Functions
We understand a set to be any collection M of certain distinct objects
of our thought or intuition (called the elements of M ) into a whole.
(Georg Cantor, 1895)
In mathematics you dont understand things. You just get used to

Chapter 5
Topology of the Real
Numbers
In this chapter, we define some topological properties of the real numbers R and
its subsets.
5.1. Open sets
Open sets are among the most important subsets of R. A collection of open sets
is called a topology, and an

Chapter 12
Applications of the Riemann
Integral
In the integral calculus I find much less interesting the parts that involve
only substitutions, transformations, and the like, in short, the parts that
involve the known skillfully applied mechanics of redu

Class 8. Mechanical energy of damped
harmonic motion
Effects of damping on the mechanical energy
The mechanical energy of the harmonic oscillator is
E=
1 2 1 2
mx + kx .
2
2
(8.1)
We can investigate how this changes with time when damping is included by

Lecture 14
Energy in Damped SHM
Quality Factor
Forced Oscillations
Resonance Width
Energy in Damped SHM
For lightly damped SHM have seen
t
x(t) = A exp cos(dt + )
2
where d =
b
m
We know that, for an undamped SH
oscillator, the total energy is
E = 21 k