Bionformatics and it's methods

tastelesscowcreekΒιοτεχνολογία

4 Οκτ 2013 (πριν από 4 χρόνια και 10 μέρες)

87 εμφανίσεις

Bioinformatics and it’s methods

Prepared by: Petro
Rogutskyi

E
-
mail: 187371@student.pwr.wroc.pl

Contents


What is bioinformatics ?


Current research in bioinformatics


Genomics:



DNA sequencing



The Human Genome Project


Proteomics: Protein Structure prediction


Comparative modeling


Interesting facts


Conclusions


Reference list

2

What is bioinformatics? (1)


Bioinformatics is a science that involves
close relation between biology and
computers that influence each other and
synergistically merging more than once.


The data is usually collected from DNA,
RNA, protein sequences

3

What is bioinformatics? (2)


Bioinformatics techniques have been
developed to identify and analyze various
components of cells, such as gene and
protein function, interactions and
methabolic* and regulatory pathways.

*
Metabolism
-

is the set of chemical reactions that happen in living
organisms to maintain life

4

Current Research in bioinformatics(1)


Genomics* sequencing and comparative
study of genomes to identify gene and
genome functionality


Proteomics


identification and
characterization of protein related
properties


*Genome is the entirety of an organism's hereditary information. It is
encoded in DNA

5

Current Research in bioinformatics(2)


Cell visualization and simulation to study
cell behavior


Application to the development of drugs
and anti
-
microbial agents

6

Genomics(1)


Genomics is the study of the collective
genetic material in an organism. This
scientific discipline is focused on
sequencing the DNA in an organism to form
a complete picture, and then identifying
specific genes in that sequence which
could be of interest.

7

Genomics(2)


In genomics, scientists analyze the DNA in
every chromosome of the organism of
interest. When a completely sequenced
set of DNA has been created, this set is
collectively known as a “genome.”


The purpose of it is to define the function
of each gene in genome

8

DNA Sequencing(1)


The raw data for the genomic analysis are
the DNA Sequences


Sequencing simply means determining the
exact order of the bases in a strand of
DNA. Because bases exist as pairs, and the
identity of one of the bases in the pair
determines the other member of the pair,
researchers do not have to report both
bases of the pair.

9

DNA Sequencing(2)

10

Chain
-
Termination Method(1)


Is the Most common method of DNA
Sequencing, used today.


This method is based on the principle that
single
-
stranded DNA molecules that differ
in length by just a single nucleotide can be
separated from one another using a
technique called
polyacrylamide

gel
electrophoresis.

11

Chain
-
Termination Method(2)


A DNA template


A primer tagged with a mildly radioactive
molecule or a light
-
emitting chemical


DNA polymerase, an enzyme that drives
the synthesis of DNA


Four
deoxynucleotides

(G, A, C, and T)


One
dideoxynucleotide
, either
ddG
,
ddA
,
ddC
, or
ddT

12

Chain
-
Termination Method(3)

13

The Human Genome Project(1)


The Human Genome Project, produced a
very high
-
quality version of the human
genome sequence that is freely available
in the internet:
http://www.ncbi.nlm.nih.gov/genbank/
.


The Sequence is derived from a some
different person’s genomes


14

The Human Genome Project(2)


The Human Genome Project was designed
to generate a resource that could be used
for a broad range of biomedical studies.


More research can then be done to fully
understand how the genome functions and
to discover the genetic basis for health
and disease.


15

Proteomics : Protein structure
prediction(1)


Genomic projects have provided large
number of sequence information


We Should obtain some benefit from this
information.

16

Proteomics : Protein structure
prediction(2)


Understanding the structural basis for
protein function enables rapid progress in
systems biology that aims at identifying
functional networks of proteins at a large
scale from genomics and proteomics
projects


Rational drug design heavily relies on the
structural knowledge of a protein

17

Proteomics : Protein structure
prediction(3)


A higher
-
level structure prediction is to
model the three
-
dimensional structure of
the protein or fold


Structure of proteins can be modeled using
comparative modeling

18

Comparative modeling


Comparative modeling involves identifying
a structural parent to an unknown
sequence and the use of geometric
constraints derived from the known
structure to model the unknown sequence


19

Software used for comparative
modeling(1)


MODELLER uses an automated approach to
comparative modeling.


COMPOSER automatically constructs
protein models using constraints derived
from structurally conserved regions (SCRs).

20

Software used for comparative
modeling(2)


MPACK (Modeling Package) is an integrated
protein
-
modeling suite designed to handle
modeling of proteins effectively


And even Web
-
based services: ESyPred3D
(
http://www.fundp.ac.be/urbm/bioinfo/e
sypred/
) That uses neural network to
improve sequence alignment. Final model
is obtained using MODELLER

21

The results of modeling

22

Interesting Facts(1)


The Chinese scientists from Hong
-
Kong
University discovered that in 1 gram of
bacteria we can encode 900 Terabytes of
information

23

Interesting Facts(2)

24

Interesting Facts(3)


Then scientists synthesize the DNA with needed
sequence end insert it into the bacteria cells

25

Interesting Facts(4)


Scientists of South Korea developed cats,
that shine under ultra
-
violet with red color

26

Interesting facts(5)


Bacteria successful in cancer treatment
that thrive in oxygen starved environments
have been used successfully to target
cancer
tumours
.


Yeast


explosive detector.

27

Interesting facts(6)


Johns Hopkins researchers have
genetically engineered the first mouse
that models both the anatomical and
behavioral defects of schizophrenia, a
complex and debilitating brain disorder
that affects over 2 million Americans.


28

Conclusions


Bioinformatics is the new science, which was created on
the intersection of biology and computer science


It’s very useful for us, because helps in disease
treatment, drugs development and better understanding
of our organism


It’s divided into different fields, such as genomics,
proteomics, etc.



For achieving special purpose the different computer
methods are used, such as chain
-
termination method or
comparative modeling

29

Reference list


M.H.
Fulekar
: Bioinformatics. Applications in life and
environmental sciences


Venkatarajan

Subramanian
Mathura,Pandjassarame

Kangueane
: Bioinformatics: a concept
-
based introduction


http://www.genome.gov/18016863


http://www.wisegeek.com/what
-
is
-
genomics.htm


http://www.daviddarling.info/encyclopedia/D/DNA_seq
uencing.html


http://2010.igem.org/files/presentation/Hong_Kong
-
CUHK.pdf


http://www.eurekalert.org/pubnews.php



30

Thank You for attention!

Questions ?

31