BIOINFORMATICS(BIOCOMPUTING)

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INTRODUCTION
DR. IBRAHIM ZAGHLOUL
IMPORTANCE OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY

Computational methods are used to study biological data because:

- Massive amount of biological data.
- Model the rules for biological processes.
- Identify important patterns.
- Visualize operations and data.
- Create simulations for biological processes.
- Predict effects and behaviors.
- Suggest mechanisms and actions
- Efficient, reduce experimental time and resources.
- Identify higher order relationships.
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 A general introduction
 – what problems are people working on?
 – how people solve these problems?
 – what key computational techniques are needed?
 – how much help computing has provided to biological research?

 A way of thinking -- tackling “biological problems” computationally

 – how to look at a “biological problem” from a computational point of view?
 – how to formulate a computational problem to address a biological issue?
 – how to collect statistics from biological data?
 – how to build a “computational” model?
 – how to solve a computational modeling problem?
 – how to test and evaluate a computational algorithm?
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WHAT IS BIOINFORMATICS?

 (Molecular) Bio-informatics
 Bioinformatics is conceptualizing biology in terms of
molecules (in the sense of physical-chemistry),
and then applying “informatics” techniques (derived from
disciplines such as applied math, CS, and statistics),
to understand and organize the information associated with
these molecules, on a large-scale.
 Bioinformatics is a practical discipline with many applications.
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SCALES OF LIFE ANIMAL CELL

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 TWO KINDS OF CELLS

 Prokaryotes – no nucleus (bacteria)

– Their genomes are circular
 Eukaryotes – have nucleus (animal,plants)
– Linear genomes with multiple chromosomes in pairs. When pairing up, they look
like

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• Differences between organisms comes from different DNA.
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DNA: THE SEQUENCE OF LIFE

 What is DNA? It is a long molecule that contains our

unique genetic code.
 It holds the instructions for making all the proteins in
our bodies.
 Made of a chemical called deoxyribonucleic acid, or
DNA for short.
 DNA contains four basic building blocks or ‘bases’:
adenine (A), cytosine (C), guanine (G) and thymine (T)
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MOLECULAR BIOLOGY INFORMATION - DNA

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GENES AND PROTEINS

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GENES AND PROTEINS

 Transcription: The enzyme RNA

polymerase uses DNA as a template
to produce a pre-mRNA transcript
and then a mature mRNA.
 Translation: mRNA is translated to
build the protein molecule
(polypeptide) encoded by the original
gene.
 The ribosome reads the mRNA to
produce a chain of amino acids.

https://www.youtube.com/watch?v=gG7uCskUOrA&t=161s
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DNA TO PROTEIN

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DNA TRANSCRIPTION

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 DNA TRANSCRIPTION

• Transcription takes place in

the nucleus.
• It uses DNA as a template to
make an RNA (mRNA)
molecule.
• During transcription, a strand
of mRNA is made that is
complementary to a strand of
DNA.

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 MRNA TRANSLATION

 Translation is the process by which a protein

is synthesized from the information
contained in a messenger RNA (mRNA).
 During translation, an mRNA sequence is
read using the genetic code, which is a set
of rules that defines how an mRNA
sequence is to be translated into the 20-
letter code of amino acids.
 amino acids are the building blocks of
proteins.
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GENES AND PROTEINS

 One gene encodes one protein.

 Like a program, it starts with start codon (e.g. ATG), then each three
code one amino acid. Then a stop codon (e.g. TGA) signifies end of the
gene.
 Sometimes, in the middle of a (eukaryotic) gene, there are introns that
are spliced out (as junk) during transcription. Good parts are called
exons. This is the task of gene finding.

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CODON TO AMINO ACID TABLE

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CODON TO AMINO ACID

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GENES AND PROTEINS

 Amino acids: the building blocks of

proteins, there are 20 different amino
acids.
 A protein: is composed of one or more long
chains of amino acids that corresponds to
the DNA sequence of the encoding gene.
 A protein is a basic structure that is found
in all of life. It’s a molecule.
 Proteins play a variety of important roles in
the body.

https://www.youtube.com/watch?v=gG7uCskUOrA&t=161s 26
AMINO ACIDS

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FROM DNA TO PROTEINS

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PROTEIN FOLDING AND STRUCTURE

• Protein amino acid sequence is folded into a 3-D

structure.
• Folding: Physical process in which the 3D structure of a
protein is formed.
• A conformation that is usually
biologically functional
• Function is related to structure:
Different structure implies
different function.
[Wikipedia]
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PROTEIN STRUCTURE

https://www.rcsb.org/structure/3ERT 30
PROTEIN FOLDING AND STRUCTURE

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GENETIC VARIANT EFFECT PREDICTION

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GENETIC VARIANT EFFECT PREDICTION

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GENETIC VARIANT EFFECT PREDICTION

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GENETIC VARIATIONS
Causes of variations
1. Mistakes in DNA replication
2. Environmental agents (radiation, chemical agents)
3. Transposable elements (transposons)
A part of DNA is moved or copied to another location in genome
4. Horizontal transfer of DNA
• Organism obtains genetic material from another organism
that is not its parent
• Utilized in genetic engineering
GENETIC VARIATIONS CONT.
Types of variations:
1. SNP (Single Nucleotide Polymorphisms)
2. Indels (Insertion-Deletion)
3. Inversion
4. Duplication

Back
 GENETIC VARIATIONS CONT.
SNP (Single Nucleotide Polymorphisms)

Ref
G A C T T C G A T C A
Sample
G A C G T C G A T C A

Back
 Synonymous
GENETIC VARIATIONS Non-synonymous SNP SNP (sSNP)
(nsSNP)

Ref G A C T T C G A T C A G DFDQ
Sample G A C G T C G A T C A A DVDQ

Back
GENETIC VARIATIONS
Indels (Insertion-Deletion)
Insertion
Ref
G A C T - - - - T C G
Sample
G A C T C G A T T C G
 GENETIC VARIATIONS CONT.
Deletion

Ref
G A C T T C G A T C A
Sample
G A C - - C G A T C A
 GENETIC VARIATIONS CONT.
Inversion

REF
G A C T T C G A T C A
Sample
G A C G C T T A T C A

Back
 GENETIC VARIATIONS CONT.
Duplication

REF
G A C G T C G A T C A
ReSeq
G A C G T C G T C C A

Back
DNA: THE SEQUENCE OF LIFE

• Nucleic acids: Chemical molecules that copy information about

fundamental determinants of life.
• DNA: is a string where each letter is a nucleotide {A, C, T, G}.
• A genome of a living organism is its entire DNA.
• Living organisms have up to trillions of cells (according to the
organism type). Each cell of the same living organism contains
the same genome.
• DNA varies in length from a few million nucleotides (bacteria)
to a few billion nucleotides (mammals).
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DNA SEQUENCE

• DNA is usually double-stranded, with one strand being the complement

of the other:
Complement of A is T Complement of C is G.
• Thus, a letter of DNA is usually called a base-pair, not a nucleotide
since, it actually represents two nucleotides: one in a DNA strand , and
one in its reverse complement strand .
• A DNA strand has a start and an end, and such direction from start to
end is important. For example, consider the following DNA:
ATGTCAGGC
TACAGTCCG
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 DNA SEQUENCE
 Each nucleotide is physically bound to its complementary nucleotide below it, forming one
base-pair.
 Assuming that the start-to-end direction of the top strand is from left to right, the start-to-end
direction of the bottom strand will be from right to left.
 Normally, we write DNA strings or substrings such that it starts at left and ends at right. Thus,
the DNA consists of two these two strands:
ATGTC and
its reverse complement: GACAT.
 When working with DNA sequences, both strands are equally
important, and they are not equivalent.
 DNA is a factory of proteins.
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 RNA

• RNA sequences is usually single-stranded and consist of letters from the

4-sized alphabet of nucleotides {A, C, U, G}.
• It exists to initiate and regulate protein production from scattered genes.
• Also, the genome of many viruses is RNA genome.

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 PROTEINS
• Proteins are short strings (few hundred letters) where each letter is one of the 20 amino
acids.
• Bacteria make around 500 to 1500 proteins , while human genome makes around
100,000 proteins .
• Each protein is produced by a gene. A gene is a fragment of the DNA.
• Every three adjacent nucleotides of a gene produces one amino acid letter of the
corresponding proteins.
• Three adjacent nucleotides are called a codon. There are 43 = 64 possible codons.
• Since 64 > 20, several different codons may produce the same amino acid.
• Also, there is a special type of codons called stop codons which indicate the end of
protein. 47
BIOLOGICAL SEQUENCES

• So far we have discussed three types of sequences, or strings, in which we are

interested
• DNA sequences which consist of letters from the 4-sized alphabet of nucleotides:
• {A, C, T, G}.
• Protein sequences which consist of letters from the 20-sized alphabet of amino acids:
• {A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V}
• RNA sequences which consist of letters from the 4-sized alphabet of nucleotides:
• {A, C, U, G}.

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OBTAINING SEQUENCES

Gene Sequences

www.ensembl.org

https://www.ncbi.nlm.nih.gov/
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OBTAINING SEQUENCES

Protein Sequences
https://www.uniprot.org/

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