BIF401 Handouts Set 3

Background of 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.

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

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.

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.

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.

Introduction to bioinformatics

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 microorganisms, 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

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.

Need for Bioinformatics – I

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.

The need for bioinformatics is on a rapid rise as biological data is rapidly increasing and becoming available online, free of any cost.

Need for Bioinformatics – II

If we observe the growth of gene bank than from 1982 it comprised of 2 billion base pairs but by year 2002 it had risen to 56 billion base pairs. With the data in our hands, there is an urgent need to interpret this data. For instance, analysis of this data can help us in developing an understanding of the phylogenetic “tree of life” which consist of:

Bacteria Archaea Eucarya

Towards exploring the possible benefits of using bioinformatics, one needs to answer the following question:

WHAT IS IT THAT BIOINFORMATICS CAN DELEIVER?

The simple answer to that bioinformatics is:

Provide us better understanding of life, evolution, molecular mechanisms as well as disease. Moreover, we can make better drugs with the availability of an enhanced molecular understanding of disease.

POSSIBLE CONTRIBUTIONS

It can help us to organize the large datasets from new experiments instruments Bioinformatics can help store and process this data as well. It can provide insights into the meanings of our research results and findings. Overall, it can help us to better understand paradoxes defining the life forms.

From gene sequencing to protein sequencing, bioinformatics is providing us with an improved understanding of the genes, proteins, protein interaction and signaling pathways involved in biological functioning and disease.

Applications of Bioinformatics – I

When we look at bioinformatics, it seems to be a very complex and abstract field. How and where can bioinformatics be applied specifically? How does it improve the fundamental understanding of biological phenomenon? Most importantly, how can its benefits be delivered to the society at large?

The answers to these questions are categorized as follows:

GENOMICS

Bioinformatics can help in assembling DNA sequencing data. It can help in gene finding (markers). Gene assembly can be performed using bioinformatics tools (nucleotide alignments) It can help transcribe the gene data to RNA data Also, databases can be generated from such data.

EVOLUTIONARY STUDIES

Evolutionary relationships between different organisms can be derived from data. Evolutionary distance among species can be computed by using bioinformatics tools. Phylogenetic trees can be constructed to find relationships between species. Ancestry can be better understood between several species and organisms.

Bioinformatics can help us in decoding protein sequences. It can also help us in understanding protein structure. We can also understand post translational changes in proteins with the help of bioinformatics. We can better understand the protein-protein interaction in different biological reactions. It can also help us in generating databases of these sequences and structures.

SYSTEMS BIOLOGY

Bioinformatics can assist us in modelling regulatory mechanisms in gene and protein networks. Such models can be analyzed to identify the key regulators in these networks. Moreover, the models can help evaluate drugs to treat these key regulators.

Bioinformatics can be applied to life in many ways it helps us to understand the sequence and function of biomolecules and their relationships. Recent trends in bioinformatics involve development of personalized therapeutics for cancer and diabetes.

Applications of Bioinformatics – II

Bioinformatics is being applied in routine life in many ways like in Genomics, transcriptomics, Proteomics, Metabolomics, Structural Proteomics, Designing Drugs, System Biology and in personalization of medicines for cure.

Except these applications Bioinformatics introduced us the techniques which enabled us to generate the large data regarding biology and also its use. And step by step the applications of bioinformatics increased from genomic level to entire system level.