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Bioinformatics Lecture1

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Bioinformatics Lecture1

Uploaded by

aarchipk
Copyright
© © All Rights Reserved
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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Textbooks

Several bioinformatics texts are available:


Baxevanis and Ouellette
David Mount
Durbin et al.
Web sites

The principal websites we will explore is NCBI:


http://www.ncbi.nlm.nih.gov
https://www.ebi.ac.uk/
https://www.ddbj.nig.ac.jp/index-e.html
Themes throughout the course:
gene/protein families

We will use biphenyl dioxygenase (BphA) as a model


gene/protein throughout the course. BphA is a member
of the ring-hydroxylating family. It is a large mw, mettaloprotein.
We will study it in a variety of contexts including
--sequence alignment
--protein structure
--phylogeny
--homologs in various species
--homology modeling and docking

We can also use other proteins.


Polychlorinated Biphenyls
• Highly Stable
• Environmentally
Persistent
• Global
contamination
• Accumulate in food
chain
• May cause cancer
& heart diseases
PCB Degradation by Proteins of
the bph pathway

BphB
Structure of BPDO
BPDO is an α3β3 hexamer that looks like a mushroom.

The α subunit constitutes the cap and the β subunit is the stem.

β
Structure of BPDO (αβ Dimer )
α
• The α subunit contains a mononuclear
iron at the active site and Rieske [2Fe-
2S] in a separate domain.
• The β subunit does not contain any
cofactor, and is not close to the active
site.

β
A molecular surface representation shows the one and
two channels to substrate binding site in B-356
(magenta) and LB400 (green) respectively.
What is
bioinformatics?
• Interface of biology and computers

• Analysis of proteins, genes and genomes


using computer algorithms and
computer databases

• Genomics is the analysis of genomes.


The tools of bioinformatics are used to make
sense of the billions of base pairs of DNA
that are sequenced by genomics projects.
bioinformati medical
cs informatic
s Tool-
users
public
health
informatics

Tool-
database algorithm makers
s s

infrastructu
Three perspectives on
bioinformatics

The cell

The organism

The tree of life

Page 4
DNA RNA protein phenotype

Page 5
Time of
development

Body region, physiology,


pharmacology, pathology
Page 5
After Pace NR (1997)
Science 276:734
Page 6
DNA RNA protein phenotype
Central dogma of molecular
biology

DNA RNA protein

genome transcriptome proteome

Central dogma of bioinformatics and


There are three major public DNA databases

EMBL GenBank DDBJ

The underlying raw DNA sequences are identical

Page 16
There are three major public DNA databases

EMBL GenBank DDBJ


Housed Housed Housed
at EBI at NCBI in Japan
European National
Bioinformatic Center for
s Biotechnology
Institute Information

Page 16
National Center for Biotechnology
Information (NCBI)

www.ncbi.nlm.nih.gov

Page 24
Fig. 2.5
www.ncbi.nlm.nih.gov Page 25
Fig. 2.5
Page 25
PubMed is…
• National Library of Medicine's search service
• 12 million citations in MEDLINE
• links to participating online journals
• PubMed tutorial (via “Education” on side bar)

Page 24
Entrez integrates…

• the scientific literature;


• DNA and protein sequence databases;
• 3D protein structure data;
• population study data sets;
• assemblies of complete genomes

Page 24
BLAST is…

• Basic Local Alignment Search Tool


• NCBI's sequence similarity search tool
• supports analysis of DNA and protein databases
• 80,000 searches per day

Page 25
Books is…
• searchable resource of on-line books

Page 26
TaxBrowser is…
• browser for the major divisions of living organisms
(archaea, bacteria, eukaryota, viruses)
• taxonomy information such as genetic codes
• molecular data on extinct organisms

Page 26
Structure site includes…
• Molecular Modelling Database (MMDB)
• biopolymer structures obtained from
the Protein Data Bank (PDB)
• Cn3D (a 3D-structure viewer)
• vector alignment search tool (VAST)

Page 26

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