Computational Biology

Lecture 1
By Safynaz AbdEl-Fattah Sayed
Computer Science Department
 Resources

• Essential Bioinformatics by JIN XIONG

• An Introduction to Bioinformatics Algorithms by NEIL C. JONES AND PAVEL A.
PEVZNER
• Bioinformatics Algorithms: An Active Learning Approach by Phillip Compeau, Pavel
Pevzner.
• https://www.youtube.com/@sarael-metwally4013
• Many other materials on the web
Assessment (100 marks)

• Course Work: 20
• Midterm: 20
• Final: 60
Course Outline
- Basic Biological Concepts

- Computational Tools & Databases & websites

- Algorithms:
- Sequence Alignment
- DNA restriction mapping
- Motif Finding

- Position-Specific Scoring Matrices (PSSM)

- Profiles and Hidden Markov Models

 Course Objectives
• Using computational algorithms to solve biological problems.

• Understanding how popular bioinformatics algorithms work.

• Understanding the methodology of algorithm’s design to identify its

potential weaknesses and fix them.

• Define the challenges that are facing the large scale biological data and
think how to solve them through developing algorithms and
bioinformatics tools.
 AGENDA
• What is Computational Biology.
• Central Dogma of Life.
• DNA, Genomes.
• RNA, Transcriptomes.
• Proteins, Proteomics .
• Transcriptions and Translation.
• Omics
Computational Biology
• Bioinformatics is computer aided biology! Also called computational biology.

• Bioinformatics is conceptualizing biology in terms of molecules and applying

"informatics techniques" (derived from disciplines such as applied maths,
computer science and statistics) to understand and organize the information
associated with these molecules, on a large scale.

+ =

Computational Biology
Biological Data Computer Algorithms
Computational Biology
• Bioinformatics is an interdisciplinary field that develops methods and
software tools for understanding biological data (Wikipedia).

• Bioinformatics is the science of collecting and analyzing

complex biological data such as genetics data.
Human Body
Genome
• Genome refers to the complete set of genetic information in an organism,
it is your DNA!
• The 23 pairs of chromosome pairs making up a human genome form 3.2
billion base pairs.
• Humans share about 99.9% of our genome.
DNA
• DNA (Deoxyribo Nucleic Acid) that carries the genetic instructions required for
the development, functioning and reproduction of all known living organisms.

• DNA holds a vast library describing how the cell works.

• It contains the instructions needed to construct other components of cell as

proteins and RNA molecules.
DNA
• In eukaryotic organisms (like animals, plants, and fungi) are multicellular,
DNA is present in the nucleus of each cell.

• In prokaryotic organisms (single-celled organisms like bacteria and

mitochondria) called unicellular, DNA is present in the cell's cytoplasm.

Prokaryotic cell Eukaryotic cell

https://sciencing.com/prokaryotic-cell-structure-13717682.html https://www.sciencetopia.net/biology/eukaryotic-cell-struct
 DNA Structure
• A nucleotide is the basic structural
unit and building block for DNA.
• A nucleotide is composed of 3 parts:
five-sided sugar
phosphate group
nitrogenous base (nitrogen containing) there are 4 bases:
Adenine (A)
Cytosine (C)
Guanine (G)
Thymine (T)
• Bases are the part of DNA that stores information and gives DNA the ability to
encode phenotype (physical characteristics of an individual, as a result of
genetic expression)
DNA Structure
• DNA is a sequence of four-letter alphabets (A, T, C, G):
TACTGTGACACTGT
• DNA is Double Complementary strand: The beginning and end of a DNA
strand are denoted 5’ (pronounced “five prime”) and 3’ (pronounced “three
prime”), respectively.
sense/forward/+/watson/code strand

anti-sense/reverse/-/crick/template strand
Chromosome
• The nucleus of human cell contains 23 chromosomes.
• A chromosome is a long, continuous piece of DNA, which contains many
genes, regulatory elements and other intervening nucleotide sequences.

Genome Human Chromosomes Human Genes

Genes
• Gene is a functional unit of DNA;
• Gene is a sequence of bases that holds genetic information and carries the
instructions to make a particular protein.
• Human genome form 3.2 billion genes.
• There are an estimated 19,000-20,000 human protein-coding genes.
• Not all of the DNA in a genome encodes protein, i.e. ~ 1.5 % of human genome
are protein coding regions.
Gene
• The gene is discontinuous, coding both:

• Exons which is a region that encodes a sequence of amino acids.

• Introns is a non-coding polynucleotide sequences that interrupts the coding

sequences, the exons, of a gene.

• Stop codons define the end of a protein.

• Genome is the complete set of DNA of an organism.

Gene Sequence
Central Dogma
• The central dogma of molecular biology is an explanation of the flow of
genetic information within a biological system. It is often stated as "DNA
makes RNA, and RNA makes protein“.
Transcription is the process of transforming information in a gene in a DNA strand to
an RNA strand, i.e. making RNA from a DNA template.
Genetic information is carried on only one of the two strands of the DNA, which known
as a coding strand.
 Transcription
RNA polymerase recognizes short
sequence of bases called promoter
sequence and bind to it.

RNA Polymerase
RNA Processing according to Gene Cell Type

https://www.cs.cmu.edu/~ckingsf/bioinfo-lectures/hmm.pdf
RNA Processing
Other RNA products
• ribosomal RNA (rRNA), which includes major constituents of
ribosomes.

• transfer RNAs (tRNAs), which carry amino acids to ribosomes.

• micro RNAs (miRNAs), which play an important regulatory role in

various plants and animals.

• mRNA
 Translation
• The nucleotide sequence of the mRNA is decoded to specify the amino acid sequence of a
polypeptide.
• This process occurs inside a ribosome and requires adapter molecules called tRNAs.
• Ribosome is the machine that synthesizes proteins from mRNA.
• Proteins are molecules composed of one or more polypeptides.
• a polypeptide is a polymer composed of amino acids.
• Cells build their proteins from 20 different amino acids.
• A polypeptide can be thought of as a string composed from a 20-character alphabet.
codons

A codon is a sequence of three DNA or RNA nucleotides that

corresponds with a specific amino acid or stop signal during
protein synthesis.
Protein Sequence

https://www.peptidesciences.com/information/peptides-vs-proteins/
Amino acid to complex
protein
 RNA vs DNA
• RNA like DNA is a string of four alphabets (U, C, A, G):

DNA RNA
• Double-stranded • Single-stranded
• Stable • Unstable
• Hard to mutate • Easy to mutate
• Storage • Storage and Function
 OMICS
• Genomics: DNA.
• Transcriptomics: RNA.
• Proteomics: Proteins.
• Metagenomics: is a new research area focused on the analysis of mixture of
DNA sequences extracted from different organisms i.e. viral, bacterial, or
eukaryotic that are living together in a symbiotic community.
• Epigenomics is the study of the complete set of epigenetic modifications on
the genetic material of a cell, known as the epigenome. The epigenome is
made up of chemical compounds and proteins that can attach to DNA and
direct such actions as turning genes on or off, controlling the production of
proteins in particular cells.
Sequencing
Prerequisite
Bioinformatics
Sample Preparation
• Due to DNA is three billions bases long &
• The sequencing machines can only sequence short (200-300 bp)
fragments.
• So, It’s important to break DNA into small fragments.
Sample Preparation

• The adapters do two things:

Allow the sequencing machine to recognize the fragments.
Allow you to sequence different samples at the same time, since
different samples have different adapters. (save time and money)
Hint: This step does not work 100% of the time (some fragments are not
recognized by machine, so they are not represented in the sample)
Sample Preparation