BIF401 Full Merged Slides Handouts 1-250

Chapter 1- Introduction to Bioinformatics

BACKGROUND

Bioinformatics is an interdisciplinary science at the cross-roads of biology, mathematics, computer science, chemistry and physics. With the digitalization of the biological information, doors have been wide opened towards the analysis of this information using computer algorithms and software.

Now we know well that the human genome has over 25,000 genes and these genes code for thousands of different proteins which perform day-to-day functions in the living cell. Furthermore, these proteins may take on various post-translational modifications leading to a very large number of functionally unique molecules. This presents us with a huge challenge in identification of genes and proteins.

Modern Biology · Humans have over 25,000 genes · The genes may produce > 250,000 different proteins · Each protein may further take up multiple modifications

But then, there are numerous organelles & intermediary molecules as well

The scale and speed of biomolecular interactions, reactions and transport is simply bewildering!

Brisk enhancements in instrumentation: · Next Generation Sequencers · High Resolution Mass Spectrometers · Nuclear Magnetic Resonance Spectroscopy · EXPERIMENTS IN BIOLOGY

With the advancements in experimental protocols, now we have several next generation instruments and techniques available for obtaining digitalized biological information on genes and proteins etc. These instruments include:

1. Next Generation Sequencers (NGS) for whole genome sequencing
2. High Resolution Mass Spectrometry for whole proteome profiling
3. Nuclear Magnetic Resonance Spectroscopy for structural studies Experiments in Biology

Brisk enhancements in instrumentation: · Next Generation Sequencers · High Resolution Mass Spectrometers · Nuclear Magnetic Resonance Spectroscopy · DIGITALIZATION OF BIOLOGY

In today’s world, when a biologist performs an experiment in the wet-lab, he or she in fact produces digital data which is continuously being stored on computer disks. The data may include text, numbers, symbols or images.

Modern biological experiments produce data which is stored on computers

The data includes text, numbers, symbols and images

SPEED OF DATA GROWTH

Due to advancement in instrumentation used in biological experiments, data is being accumulated at exponentially increasing rates. For example; genome sequences in genome databases are doubling every few years.

Data is being accumulated at an exponentially increasing rate

E.g. Genome sequences in genome databases are doubling every few years!

Human brain is limited in recalling information from memory. First, we have to commit all information to our memory followed by its recall. To overcome our ability to memorize and recall, computers can come to our rescue. This is because computers have an infinite ability to recall this information and process it quickly towards results.

Humans are limited in recalling information from their memory

So, we need the help of computers to store and recall this data!

Computers can also quickly process this information and help in its manipulation.

MOTIVATION

Bioinformatics is a becoming a popular science due to several reasons.

➢ It is an interdisciplinary field as it covers the information of biological digital information including human, plants, animals and microorganisms. ➢ Although it is a new field but it is rapidly developing field. ➢ It demands a very low cost infrastructure and hardly any lab equipment. ➢ As bioinformatics data concerns a wide range of species such as humans, plants and micro-organisms, it presents us with plenty of opportunities in scientific discovery.

SCOPE OF BIOINFORMATICS

Bioinformatics primarily deals with digitalized biological information as well as data reported from biology experiments. Computational methods, data processing techniques and algorithms are employed in addressing the following issues:

➢ Storage of data · ➢ Organization data · ➢ Analysis of many experiments · ➢ For representation of biological information · ACTIVITIES

In modern biological sciences, bioinformatics is used for activities such as:

➢ Developing algorithms for organizing data collected from experiments ➢ Writing software and tools for data analysis ➢ Data processing to determine the role of underlying biomolecules ➢ Statistical evaluation of data using methods such as t-test and ANOVA

➢ Data visualization for meaningful presentation of biological information

Moving ahead…

Learn the available bioinformatics concepts, algorithms and tools

Advance these concepts by developing novel ideas

Apply these ideas to forward the understanding of biology and life

In Pakistan, the field of biology is undergoing a rapid change due to the onset of bioinformatics. New research and educational programs are being constructed which is opening new door of opportunities for our future generations.

The benefits of studying bioinformatics in Pakistan

New degree programs in several universities

Opportunity for cutting edge discoveries in a resource-limited setting

• NEED FOR BIOINFORMATICS –I

If we look at the pace of development in the area of bioinformatics then we can easily observe that from year’s 2000 to 2015, the number of online tools for processing genomics and proteomics information are rapidly increasing. This is just a reflection of the need for bioinformatics in modern day biology.

The field of Bioinformatics and Computational Biology is characterized by a highly diverse confluence of traditional academic disciplines. Informatics and Bio-science are the umbrella terms given to a set of allied disciplines which make up the field, but a much larger array of traditional areas contribute to the set of tools needed by individuals training for this new and expanding interdisciplinary field. Biomedical Engineering, Electrical and Computer Engineering, Computer Science, Applied Mathematics, Genetics, Biology, Anatomy and Cell Biology, Micro Biology, and Biostatistics are the principal allied disciplines.