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: habeeb_skm@yahoo.co.in
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