1. Introduction to Bioinformatics

8/19/2019 1. Introduction to Bioinformatics

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(Bioinformatics) ____________________

the intersection of

Information technology&

Biology

Ahmed A. Zayed


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How much

informationdoes our

body hold ??


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The smallest amount of

information can be

obtained from a YES / NO

question

With

1 / 0

Answer

i.e.

1 Bit of information


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Our genetic code is made of 4 nucleotides each

can be represented by:

2 Bits of information


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Our entire genetic code can be

stored in a single DVD !!!!


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40,000,000,000,000 cells in body

X 1.5 GB

=60 zettabytes

60 X 1021

All the information our

civilization stores will

reach only 40 ZB by

2020

It can be stored in less

than 100 gm of DNA!!!!


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Introduction to(Bioinformatics)

____________________

Molecules of life

Ahmed A. Zayed

Part 1

Part 2


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Introduction to

(Bioinformatics)


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What is Bioinformatics?

It is about :•searching biological

databases,

•comparing sequences,

•looking at protein

structures,

•and asking

biological questions

with a computer


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Bioinformatics is vastly growing that !!!!!!


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Shortly, Bioinformatics is the:

of large-scale, complex

&

using

•Storage

•Retrieval

Papers, Sequences,

and structures of

(DNA, Proteins)

• Analysisconverting sequences into gene

•ModelingProtein structure predictions


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We, as END USERS

Can perform biological experiments

in vivo ,

within a living organism.

in vitro ,

(in glass) or in an artificial environment.

in silico ,

through silicon chips (bioinformatics)


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Theory of molecular

evolution

phylogenies based on

sequence comparison

differences between

homologous sequences

as a molecular clock to

estimate the time since

the last common ancestor

Linus Pauling


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phylogenies based on

sequence comparison


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Atlas of Protein Sequence

The first comprehensive,

computerized and

publicly available

collection of protein

sequences.

It became a model formany subsequent

sequence databases,

including GenBank.Margaret Oakley Dayhoff


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Needleman-Wunschalgorithm

Global sequence alignment


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DNA

sequencingand

software to

analyze it

(Staden

software)

DNA sequencing andStaden software

Modern version of Staden software


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1- All basic sequence alignments programs.

2- Phylogenetic and classification methods.

3-Various display tools adapted to relatively

small sequence objects

(such as protein sequences of, at most, a fewthousand characters long).

Most of the bioinformatics softwares

(tools) include:


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Smith-Waterman algorithm

Smith and Waterman

Local sequence

alignment


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Sequence

alignment


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Local sequence

alignment

Global sequence

alignment


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The concept of a sequencemotif

Nucleotide or amino-acid sequence

pattern that is widespread and has, or is

conjectured to have, a biologicalsignificance.

A DNA sequence motif represented as a sequence logo

graphically representing the observed probabilities


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GenBank Release 3 madepublic

open access, annotated collection of all

publicly available nucleotide sequences andtheir protein translations

http://www.ncbi.nlm.nih.gov/genbank/


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Phage lambda genomesequenced

Bacteriophage lambda

Provided useful tools

in molecular genetics

such as being used as a

vector for the cloning

of recombinant DNA


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Sequence databasesearching algorithm

David J. Lipman

Allowed searchingthe fast growing

huge databases


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FASTP /FASTN: fastsequence similarity

searching

FASTA format for nucleotide sequence

>gi|5524211|gb|AAD44166.1| cytochrome b

LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGY

>gi|1045243| cytochrome bACTGATCATAGTACATGACATAGATATCAGATACATAGAC

FASTA format for amino-acid sequence


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Searching NCBI’s Literature Databases

Activity 1

http://www.ncbi.nlm.nih.gov/gquery


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EMBnet network fordatabase distribution

Synchronizing the data

between databases every

night!!!


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BLAST: fast sequencesimilarity searching

http://blast.ncbi.nlm.nih.gov/Blast.cgi

Basic Local Alignment Search Tool


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EST: expressed sequencetag sequencing

short sub-sequence of a cDNA sequence.

They may be used to identify

gene transcripts, and are instrumental in

gene discovery.


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Sanger Centre, Hinxton,UK

charitably funded genomic

research centre , A leader inthe Human Genome Project

EMBL European

Bioinformatics Institute

http://www.ebi.ac.uk/

http://www.embl.de/


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First bacterial genomes completely

sequenced

Yeast genome completely sequenced

Worm (multicellular) genome

completely sequenced

Fly genome completely sequenced

Human genome project is

complete

http://www.sanger.ac.uk/Projects/C_elegans/http://www.sanger.ac.uk/Projects/C_elegans/http://www.sanger.ac.uk/Projects/C_elegans/


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Thank You

Questions ?

Documents

1. Introduction to Bioinformatics