Download BME435 BIOINFORMATICS

BME435
BIOINFORMATICS
BIOINFORMATICS
Section 1: Introduction and biological databases.
Section 2: Sequence alignment.
Section 3: Gene and promoter prediction.
Section 4: Molecular phylogenetics.
Section 5: Structural Bioinformatics
Section 6: Genomics and Proteomics
Section 1: Introduction and biological
databases
1- Introduction
What is BIOINFORMATICS?
Goal/Scope
Applications
Limitations
New Themes
WHAT IS BIOINFORMATICS?
 Bioinformatics is an interdisciplinary reseach
area at the interface between computer science
and biological science.
 Increasingly popular field - There is a very high
demand for bioinformaticians both in industry and
in academia.
BIOINFORMATICS involves the technology
that uses computers for
 Storage,
 Retrieval,
 Manipulation,
 Distribution of information related to
biological macromolecules such as DNA,
RNA, and proteins.
HOW BIOINFORMATICS DIFFERS FROM A RELATED
FIELD KNOWN AS COMPUTATIONAL BIOLOGY?
 BIOINFORMATICS is limited to
 Sequence,
 Structural and functional analysis od genes and
genomes and their corresponding products.
 COMPUTATIONAL BIOLOGY encompasses all
biological areas that involve computation.
 E.g. Mathematical modelling of ecosystems
 Population dynamics,
 Application of Game theory in behavioral studies.
GOALS and SCOPE
GOALS:
 Better understand the living cell
 How it functions at the molecular level.
 Solving functional problems using
sequence and sometimes structural
approaches has proved to be a fruitful
endeavor.
SCOPE:
 Bioinformatics consists of two subfields:
 The development of computational tools
and databases.
 The application of these tools and
databases in generating biological
knowledge to beter understand living
systems.
Overview of various subfields of
bioinformatics
The applications of the tools fall into three
areas:
 Sequence analysis,
 Structure analysis,
 Function analysis.
APPLICATIONS
Structure Analysis
•Nucleic acid structure
prediction
•Protein structure
prediction
•Protein structure
Classification
•Protein structure
comparison
Sequence Analysis
Function Analysis
•Genome comparison
•Phylogeny
•Metabolic pathway
modelling
•Gene & promoter
prediction
•Gene expression
profiling
•Motif discovery
•Protein interaction
prediction
•Sequence database
Searching
•Sequence alignment
•Protein subcellular
localization
prediction
SOFTWARE DEVELOPMENT DATABASE CONSTRUCTION AND CURATION
APPLICATIONS
• BIOINFORMATICS having a major impact on
many areas of biotechnology and biomedical
sciences.
e.g.
• Knowledge-based drug design,
• Forensic DNA analysis,
• Agricultural biotechnology.
LIMITATIONS

Bioinformatics has a number of inherent limitations.

Bioinformatics is by no means a mature field.

Most algorithms lack the capability and sophistication to truley reflect the
reality.

Errors in sequence alignment, an affect the outcome of structural or
phyligenetic analysis.

Many accurate but exhausitive algorithms cannot be used because of the
slow rate computation. Instead, less accurate but faster algorithms have to
be used.

IT IS A GOOD PRACTICE TO USE MULTIPLE PROGRAMS, IF THEY
ARE AVAILABLE, AND PERFORM MULTIPLE EVALUATIONS.

A MORE ACCURATE PREDICTION CAN OFTEN BE OBTAINED IF ONE
DRAWS A CONSENSUS BY COMPARING RESULTS FROM DIFFERENT
ALGORITHMS.
NEW THEMES
 There is no doubt that bioinformatics is a field that holds
great potential for revolitionizing biological research in
the coming decades.
 The field is undergoing major expansion. In addition to
providing more reliable and more rigorous
computational tools for sequence, structural and
functional analysis.
 THE MAJOR CHALLENGE FOR FUTURE
BIOINFORMATICS DEVELOPMENT IS TO DEVELOP
TOOLS FOR ELUCIDATION OF THE FUNCTIONS
AND INTERACTIONS OF ALL GENE PRODUCTS IN A
CELL.