Advanced Bioinformatics
Course code BIO-7505
Course Instructor
Dr. Samar Naseer
Why bioinformatics?
What is Bioinformatics?
• The term bioinformatics was coined in 1978 (Paulein
Hogeweg 1978) and was defined as the “study of informatic
processes in biotic systems”
• Bioinformatics is the unified discipline formed from the
combination of biology, computer science, and information
technology
• Bioinformatics is often defined as “the application of
computational techniques to understand and organise the
information associated with biological macromolecules”
CONT…
• Bioinformatics differs from a related field known as computational
biology
• Computational Biology refers to the aspect of developing
algorithms (mathematical formulas) and statistical model which is
necessary to analyze biological data through the aid of computers
• Bioinformatics however involves the technology that uses
computers for storage, retrieval, manipulation, analysis, and
distribution of information related to biological macromolecules such
as DNA, RNA, and proteins
CONT…
• Twenty years after the term bioinformatics had been coined,
another term, chemoinformatics, was published (Brown
1998)
• It is that branch of bioinformatics that deals with the study of
chemical compounds produced within organism specially
secondary metabolites produced in plants
• The term chemoinformatics OR cheminformatics, is used as
an umbrella term that even includes additional terms like
molecular modelling
What can Bioinformatics do….
✓ sequence alignment
✓ gene finding
✓ genome assembly
✓ Single Nucleotide Polymorphism (SNPs) identification
✓ protein structure alignment
✓ protein structure prediction
✓ predict products of gene expression
✓ protein-protein interactions
✓ gene expression profiling
✓ biochemical pathways
✓ Construct phylogeny
What can Bioinformatics do….
✓ post-translational modifications
✓ transcriptome analysis
✓ to identify and structurally modify a natural product
✓ to design a compound with the desired properties
✓ to assess therapeutic effects of a compound
✓ drug discovery and drug development
✓ the modelling of evolution
✓ And many more such analysis
Components of Bioinformatics
Bioinformatics comprises three components
1. Creation of databases
2. Development of algorithms and statistics
3. Analysis of data and interpretation
CONT….
1. Creation of databases:
• This involves the organizing, storage and management
of the biological data sets
• The databases are accessible to researchers to know
the existing information and submit new entries, e.g.
protein sequence data bank for molecular structure,
genbank, etc
• Databases will be of no use until analysed
CONT…
2. Development of algorithms and statistics
• This involves the development of tools and resources to
determine the relationship among the members of large
data sets
• e.g. comparison of protein sequence data with the
already existing protein sequences
CONT…
3. Analysis of data and interpretation
• The appropriate use of components to analyse the data
and interpret the results in a biologically meaningful
manner
• This includes DNA, RNA and protein sequence analysis,
protein structure analysis, gene expression profiling and
biochemical pathways, etc.
Level of Organization in Bioinformatics
There are two sub-fields in bioinformatics:
1. Computational Bioinformatics
• It refers to all the computational work done to develop an application
that is aimed to address certain problems in biology
• Computational Bioinformatics further has the following levels:
➢ Algorithm and Software Development: To solve any problem we
first must have a strategy to tackle the problem. For this, algorithm
of the application is a must. Here people with different expertise
work together to develop an algorithm
CONT…
➢ Database Construction and Curation:
• Any information generated in the lab must be stored in a database
for easy retrieval in the future
• Database is a place where one can store related information which
makes the information much more meaningful and help in the future
development
• There are countless public databases that focus on different levels
or types of biological information
2. Application Bioinformatics
Various bioinformatics application can be categorized
under following groups:
1. Sequence Analysis
2. Function Analysis
3. Structure Analysis
CONT….
• Sequence Analysis: All the applications that analyze various
types of sequence information and can compare similar types
of information is grouped under Sequence Analysis
• Function Analysis: These applications analyze the function
contained within the sequences and helps to predict the
functional interaction between various proteins or genes
• Structure Analysis: It is devoted to predict the structure and
possible roles of the structures of proteins or RNA
Branches of Bioinformatics
Bioinformatics is broadly divided into
three closely related branches
1. Genomics
2. Transcriptomics
3. Proteomics
Genomics
• The study of structure and function of entire genome of an
organism is referred to as genomics
• In genomics, the nucleotide sequences of all the
chromosomes of an organism are mapped and the location of
different genes and their sequences are determined
• This involves extensive analysis of the nucleic acids through
molecular biology techniques before the data are ready for
processing by computers
• Genomics uses the techniques of molecular biology and
bioinformatics to identify cellular components such as DNA,
rRNA, tRNA, etc., and analyse the sequences attributed to the
structural genes, regulatory sequences, and even non-coding
sequences
CONT…
The discipline of genomics consists of three groups:
(i) Comparative genomics
(ii) Structural genomics
(ii) Functional genomics
CONT…
1. Comparative genomics: It deals with the finding differences and
similarities between the whole genome of multiple species to know
about species and its evolution
2. Structural Genomics: It deals with the study of the structure of
entire genome of an organism.
In other words, it deals with the study of the genetic structure of each
chromosome
3. Functional Genomics: It deals with the study of genome function. It
deals with transcriptome and proteome
CONT…
❑ The insertion of the crystal protein genes from Bacillus thuringiensis in
the genomes of several crop plants for pest resistance is the outcome
of functional genomics
❑ Functional genomics also helps us to understand the function of human
genes, the genes of the rice plant, and other organisms
❑ Also helps to Identify genes responsible for production of specific
antibodies and produce vaccines
❑ It is now possible to identify the genes responsible for pathogenesis in
the genomes of parasites and to produce DNA vaccines based on this
information
Proteomics
• Proteomics refers to the study of structures and functions of all
proteins in an individual
• In other words, it deals with the study of entire protein expressed in
an organism
• Proteomics is of two types:
1. Structural proteomics
2. Functional proteomics
CONT…
1. Structural Proteomics: It refers to the study of the structures of all
proteins found in a living organism
2. Functional Proteomics: It deals with functions of all proteins found
in a living organism
➢ In fact, proteomics is a sub-discipline of functional genomics. It is
the study of proteomes, which refer to complete set of proteins
encoded by a genome
➢ A variety of techniques are used for the study of proteomics
Transcriptomics
• Transcriptomics is the study of the
transcriptome, which includes the whole set
of mRNA molecules (or transcripts) in an
organism or a population for a given set of
environmental circumstances
• This study helps us to depict the expression
level of genes, often using techniques such
as DNA microarrays, that is capable of
sampling tens of thousands of different
mRNAs at a time.
• This kind of new technique has helped
biologists to routinely monitor the gene
expression of cells over time