Overview of Bioinformatics

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Overview of Bioinformatics
BY DR.C. AMRUTHAVALLI HOD OF BIOINFORMATICS CIST U
NIVERSITY OF MYSORE
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• Bioinformatics is the field of science in which
  molecular biology, statistics, computer science,
  and information technology merge into a single
  discipline.
• Bioinformatics is the science of managing and
  analyzing molecular biology data using advanced
  computing techniques.
• Bioinformatics is the computer-assisted data
  management discipline that helps us
• Gather, store, analyze, integrate biological and
  genetic information (data), and represent this
  information efficiently.
• Bioinformatics is the electronic infrastructure
  of molecular biology

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Software of Bioinformatics There are many
different bioinformatics tools available over the
Internet free of charge to whomever wishes to use
them. There are also many commercial software
packages used in bioinformatics by researchers
who can afford it. The number of software
products is growing constantly, so that it is
impossible to list, as software developers
working in the life sciences (or life scientists
with software development talents), are
constantly updating and producing useful new
applications. Development and implementation of
tools that enable efficient access and management
of different types of information, such as
various databases, integrated mapping
information
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Bioinformatics is associated typically with
massive databases of gene and protein sequence
and structure/function information databases.
New sequences, new structures or protein/gene
function that are discovered are searched,
(compared) against what is already known,
(gathered), and deposited into the databases.
(These searches are done by remote computer
access using various bioinformatics tools.)
Analysis and interpretation of various types of
biological data including nucleotide and amino
acid sequences, protein domains, and protein
structures. Development of new algorithms and
statistics with which to assess biological
information, such as relationships among members
of large data sets.
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What type of information do we deal with in
bioinformatics? DNA (Genome) RNA
(Transciptome) Protein (Proteome) Sequence
Structure Evolution Pathways Interactions
Mutations
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DNA Simple Sequence Analysis Database
searching Pairwise analysis Regulatory Regions
Gene Finding Whole Genome Annotations
Comparative Genomics (Analyses between Species
and Strains )
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RNA Splice Variants Tissue specific expression
Structure Single gene analysis (various
cloning techniques) Experimental data involving
thousands of genes simultaneously DNA Chips,
MicroArray, and Expression Array Analyses
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Protein Proteome of an Organism 2D gels Mass
Spec 2D Structure 3D Structure
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Sequence Analysis Software What is the
information contained in a biological
sequence? How can we analyze it to gain
knowledge? Does it contain any functional
clues?
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Biological problems that computers can help
with I cloned a gene - is it a known gene?
Does the sequence match? Is the sequence any
good? Does it look like anything else in the
database? Which family does it belong to? How
can I find more family members? I have an orphan
receptor, how can I find its ligand? The gene
Iím interested in was found in another organism,
but not mine. How can I look for it? I have
linkage to a specific region on chromosome x,
how do I find genes in that region?
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The Potential of Bioinformatics The potential
of Bioinformatics in the identification of useful
genes leading to the development of new gene
products, drug discovery and drug development has
led to a paradigm shift in biology and
biotechnology-these fields are becoming more
more computationally intensive. The new paradigm,
now emerging, is that all the genes will be known
"in the sense of being resident in database
available electronically", and the starting point
of biological investigation will be theoretical
and a scientist will begin with a theoretical
conjecture and only then turning to experiment to
follow or test the hypothesis. With a much deep
understanding of the biological processes at the
molecular level, the Bioinformatics scientist
have developed new techniques to analyse genes on
an industrial scale resulting in a new area of
science known as 'Genomics'.
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Bioinformatics - Industry Overview The
Bioinformatics industry has grown to keep up with
the information explosion, growing at 25-50 a
year. In 2000, the US market Research company
Oscar Gruss estimated that the value of the
Bioinformatics industry would touch 5 billion.
Now it s demand for individuals capable of doing
bioinformatics is soaring. Industry's demand for
scientists with skills in Bioinformatics far
exceeds the supply of qualified specialists in
the field, Seems likely that this figure will be
reached within the coming year. Therefore,
companies are developing methods of spotting
potential Bioinformatics experts and then
training them on the job.
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Assigning fold and function utilizing similarity
to experimentally characterized proteins

• Sequence similarity BLAST and others
• Beyond sequence similarity matching sequences
  and shapes (threading)

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• Aims of Bioinformatics
• The aims of bioinformatics are basically
  three-fold. They are
• Organization of data in such a way that it allows
  researchers to access existing information to
  submit new entries as they are produced. While
  data-creation is an essential task, the
  information stored in these databases is useless
  unless analyzed. Thus the purpose of
  bioinformatics extends well beyond mere volume
  control.
• To develop tools and resources that help in the
  analysis of data. For example, having sequenced a
  particular protein, it is with previously
  characterized sequences. This requires more than
  just a straightforward database search. As such,
  programs such as FASTA and PSI-BLAST much
  consider what constitutes a biologically
  significant resemblance. Development of such
  resources extensive knowledge of computational
  theory, as well as a thorough understanding of
  biology.
• Use of these tools to analyze the individual
  systems in detail, and frequently compared them
  with few that are related.

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• Analysis activity in Bioinformatics
• Development of methods to predict the structure
  and/or function of newly discovered proteins and
  structural RNA sequences.
• Clustering protein sequences into families of
  related sequences and the development of protein
  models.
• Aligning similar proteins and generating
  phylogenetic trees to examine evolutionary
  relationships

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Sub-disciplines within bioinformatics There are
three important sub-disciplines within
bioinformatics involving computational biology
The development of new algorithms and statistics
with which to assess relationships among members
of large data sets The analysis and
interpretation of various types of data including
nucleotide and amino acid sequences, protein
domains, and protein structures and The
development and implementation of tools that
enable efficient access and management of
different types of information
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• Medical applications
• Understand life processes in healthy and disease
  states.
• Genetic Disease (SNPs)
• Pharmaceutical and Biotech Industry
• To find (develop) new and better drugs.
• Gene-based or Structure-based Drug Design
• Agricultural applications
• Disease, Drought Resistant Plants
• Higher Yield Crops

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Careers in Bioinformatics Genomics Genome
sequencing of Bacteria, viruses Animals
Plants Comparative genomics Annotation and
Mapping Gene Discovery Functional Genomics
(Gene Expression and Regulation) Control
Regions Switches Circuits Bypass Feedback
loops Environmental Effects Diseased States
Chemical Consequences
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Careers in Bioinformatics Pharmacogenomics
SNPs Regional, ethnic variations Inheritance
patterns Radiological/ecological
modifications Therapeutic target recognition
Correlation of drug and expression effects
Pathway Effects Proteomics Protein Profiling
Alternate splice variants Orphan genes
Cryptic introns Gene Therapy
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Careers in Bioinformatics Structural Genomics
Experimental Protein structures Apo state
Holo state Structural modifications Membrane
Proteins Homology Modelling Comparative
Modelling Drug and Vaccine Design Screening
Natural Products Plants, Fungi Bacteria
Chemicals In silico modifications of ligands
Vaccine design and delivery
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Conclusion With the confluence of biology and
computer science, the computer applications of
molecular biology are drawing a greater attention
among the life science researchers and scientists
these days. As it becomes imperative for
biologists to seek the help of information
technology professionals to accomplish the ever
growing computational requirements of a host of
exciting and needy biological problems, the
synergy between modern biology and computer
science is to blossum in the days to come. Thus
the research scope for all the mathematical
techniques and algorithms coupled with software
programming languages, software development and
deployment tools are to get a real boost. In
addition, information technologies such as
databases, middleware, graphical user
interface(GUI) design, distributed object
computing, storage area networks (SAN), data
compression, network and communication and remote
management are all set to play a very critical
role in taking forward the goals for which the
Bioinformatics field came into existence.
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The genomics revolution has transformed the
landscape of drug discovery. DNA and protein
sequences are yielding a host of new therapeutic
targets and an enormous amount of associated
information. The challenges in the genomics arena
are to securely and reliably manage and analyze
huge quantities of sequence and associated data,
and to extract useful information from that
data Detailed study of the three dimensional
molecular structure of DNA, proteins, and other
biological compounds can be critical to
understanding their function and to designing
therapeutics to control their effects. Modeling,
simulation, and other computational techniques to
predict and analyze this structure are essential
components in today's discovery research
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Thank you
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Significance of protein folding problem
VLSEGEWQLVLV . . .

• O2

Sequence structure
function
folds into a 3D
to perform a