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Computational Biology & Bioinformatics

By G.S.JeraldJasper

Biological Data + Computer Calculation

Why Bioinformatics?
Study

and manage biological data.

Answer

complex biological questions.


the computation speed and

Improve

accuracy.
converting

data to information.

Bioinformatics defined
Bioinformatics

is broad term covering the use of

computer algorithms to analyze biological data.

Computational

biology is a techniques to model

biological systems at various levels of complexity atomic, metabolic, cellular and pathologic

Bioinformatics Data
DNA

sequences

Protein

Sequences

Protein/RNA

structures

Gene

expression

Biological Databases

Almost

all biological data are stored, managed,

and annotated in databases that are publicly accessible.


Data

are often shared between different

databases.

Important databases
Text

formats are provided by PubMed and OMIM.

Sequence

data is provided by GenBank, in terms of

DNA, and UniProt, in terms of protein.

Protein

structures are provided by PDB, SCOP,

and CATH.

Database growth

Central Paradigm for Bioinformatics

Genomic Sequence Information

Protein Structure

Protein Function

Phenotype (Symptoms)

Areas in Bioinformatics
Genomics Proteomics Protein

Structure Prediction

Phylogenetic

Genetic vs Genomics

Genetics

is the Study of genes

Genomics

is the study of

, heredity , and variation in living organisms.

functions and interactions of all the genes in the genome, including their interactions with environmental factors.

Genomics - Finding Genes


Gene

in sequence data needle in a haystack as the needle is different from the haystack

However

genes are not different from the rest of the sequence data
This

is one of the challenges of bioinformatics


networks and dynamic programming are

Neural

being employed

Organism

Genome Gene Size Number (Mb)


bp * 1,000,000

Web Site

Yeast

13.5

6,241

Fruit Flies

180

13,601

Homo Sapiens

3,000

45,000

http://genomewww.stanford.ed u/Saccharomyce s http://flybase.bio. indiana.edu http://www.ncbi.n lm.nih.gov/geno me/guide

Proteomics
Proteome

is the sum total of an organisms

proteins
More

difficult than genomics

Protein Structure Prediction

Is one of the biggest challenges of bioinformatics and

especially biochemistry

No algorithm is there now to consistently predict the structure of proteins

Phylogenetics
The

taxonomical system reflects evolutionary relationships Phylogenetic tree reconstruction algorithms are also an area of research

Applications

Medical
Pharmacogenomics

Customized treatment

Gene Therapy

Replace or supply the defective or missing gene


E.g: Insulin and Factor VIII or Haemophilia

Bioweapons (??)

Plague, smallpox, anthrax,..

Other Applications..
Diagnosis

of Disease

Identification of genes which cause the disease will help detect disease at early stage.

Drug

Design

Can go up to 15yrs and $700million

One of the goals of bioinformatics is to reduce the time and cost involved with it.
Computational methods can improves this

Target

identification
the molecule on which the germs relies for

Identifying

its survival Then we develop another molecule i.e. drug which will bind to the target So the germ will not be able to interact with the target. Proteins are the most common targets

For example HIV produces HIV protease which is a protein and which in turn eat other proteins This HIV protease has an active site where it binds to other molecules So HIV drug will go and bind with that active site

Related Computer Technology

Matlab(Bioinformatics toolbox) Biojava BioPerl XML and web Services BioPython