Introduction to bioinformatics by Habeeb

8/8/2019 Introduction to bioinformatics by Habeeb

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HABEEB. SKMDEPT OF BIOINFORMATICS

GURU NANAK COLLEGE

CHENNAI


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DEFINITION

WHAT

WHY

HOW

TOOLS & DATABASES

BASIC PROTOCOL : SEQUENCE ANALYSIS

SICKLE CELL ANEMIA

DRUG DISCOVERY & BIOINFORMATICS

BIOINFORMATICS


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Levels of Protein Structure


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FUNCTIONS OF PROTEINS


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Need for Bioinformatics

Genomes are the complete set of chromosomesof organism, which contain its full DNA,genes & lots of junk DNA.

Still a lot of genomes to be sequenced,considering the 1.8 million classified species,and the possibility of existing 10 to 100million unknown.

Advanced Research Trends especiallysequencing genome projects have resulted inhuge amounts of raw data that must bestored, manipulated and analyzed.


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Narrow Definition: The use of computer tools to store, access and analyze nucleic acid data

and amino acid data and protein structure data.

A broad Definition:

The use of computer tools to store, access and analyze all types ofbiological data.

Personal Definition:

The utilization of computation for biological investigation and

discoverythe process by which you unlock the biological world

through the use of computers.

Data: text data, phylogenetic trees and metabolic maps

Many applications in Biological Research, Drug design and Medicine


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Bioinformatics is associated typically with massive

databases of gene and protein sequence and

structure/function information databases.

Analysis and interpretation of various types of

biological data.

Development of new algorithm and statistics with

which to assess biological information.

Development and implementation of tools.


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Role for Bioinformatics


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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

Bioinformatics: Sequence Analysis


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DATABASES & TOOLS

GENBANK

DDBJ

EMBL

SWISSPROT

UNIPROT

TrEMBL

PDB

SCOP

CATH

ATLAS

PROSITE PFAM

BLOCKS PRINTS

KEGG

BRITE

IMGDB

EXPASY

COG

BLAST

FASTA

BLOSUM

PAM

GONNET

RASMOL CN3D

SW ISSPDBVIEWER VMD

NEURALNETWORKS

HMM

CHOUFASMAN

GOR

AB INITIOMETHOD

THREADING

HOMOLOGYMODELING

CLUSTAL

T-COFFEE

PHYLIP

PAUP


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Scoring Matrices: PAM & Blosum


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HUMAN GENE MUTATIONDATABASE (HGMD)


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These databases help us in carrying out our research.

Huge amount of ever growing data.

Numerous databases under same category to confirm predictions.

Structure prediction with bioinformatics is so easy that it can bedone in few minutes to few hours.

Its a field with lots of potential to help research in diverse fields.

Structural properties can easily be predicted.

Many tools are available to understand the interaction betweenthe target protein and the ligand such as Autodock, iGemdock,Arguslab, Hex.

Incase, the chemical structure of the ligand is not present in thechemical structure databases it can be drawn using various

structure drawing softwares viz, ISIS Draw, Chemsketch.


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A practical Approach:

Short DNA fragment: 10 20 300 GAGGAGAAGT CTGCCGTTAC TGCCCTGTGG

Six-frametranslation:

Forward0: EEKSAVTALW Forward1:RRSLPLLPC

Forward 2 : GEVCRYCPV Reverse0: PQGSNGRLLL

Reverse1: HRAVTADFS Reverse 2 :TGQ!RQTSP

OWL Database Hits: 29

HBB2_PANLE HEMOGLOBIN BETA-2 CHAIN. - PANTHERA LEO(LION).MW=15855.115900 LEN=146 Mol. wt. (calc) = 15855.1Residues = 146

00 G H L T P E E K S A V T A L W S K V N V D E V G G E A L G R

31 L L V V Y P W T Q RFF E S F G D L S T P D A V M G N P K V

61 K A H G K K V L G A F S D G L A H L DN L K G TF A T L S E

91 L H C D K L H V D P E NFR L L G N V L V C V L A H H F G K121 E FT P P V Q A AY Q K V V A G V A N A L A H KY H


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Family Search Results

Scan Prosite


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Family Search Results contd:


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Top 5 Fingerprint results with motifs


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Alignment of Beta Hemoglobin entries of Printscan results:


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Sickle cell anaemia- due tochange in one base pair

CCTGATCC (Valine)

CCTGTTCC(Glutamine)


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Phylogeny of HBB


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Betterunderstandallorganisms.

Helpsindiseasediagnosisandprevention

Helpsunderstandourresponsetotreatments,creatingthepossibilityofcustomizedones

Identificationofdrugtargets

GeneTherapy

Moreadvancesinspecifictreatment

A bettercomprehensionofourbodies

A bettercomprehensionoftherelationships betweenorganisms


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Discovernewdrugtargetscomputationaldocking


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HIV PROTEASE & INHIBITOR


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Therecentenormousincreasein biologicaldatahasmadeitnecessaryto

usecomputers,informationtechnologytocollect,organize,maintain,access

andanalyzedata.

Computerspeed,memory,exchangeofinformationovertheinternethasgreatlyfacilitated bioinformatics.

The bioinformaticstoolsavailableovertheinternetareaccessible,well

developed,fairlycomprehensiveandrelativelyeasytouse.

Conclusion


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You can reach me at:

Email: [email protected]

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Introduction to bioinformatics by Habeeb