What is Bioinformatics?

Bioinformatics is a great improvement in technology. It has numerous benefits in today’s world. In this guide, we will discuss bioinformatics and its benefits. If you are interested in knowing more about it, you should read through this guide.

What is Bioinformatics?

Bioinformatics is an emerging branch of biological science that emerged from the combination of both biology and information technology. It is an interdisciplinary field of study that uses Biology, Chemistry, Mathematics, Statistics, and Computer Science that have merged to form a single discipline. This sector is mainly involved in analyzing biological data, and developing new software using biological tools.

According to the NCBI- National Center for Biotechnology Information, the branch of NLM- National Library of Medicine and NIH- National Institutes of Health, Bioinformatics is defined as the analysis, collection, classification, manipulation, recovery, storage, and visualization of all biological information using computation technology.

The term Bioinformatics was first coined in the year 1960 by two Dutch biologists named Paulien Hogeweg and Ben Hesper. According to their research and discoveries, Bioinformatics was defined as the study of information processes in biotic systems.

Bioinformatics is important because experiments do not exist in a vacuum. The 2020 coronavirus pandemic shows that rapid data analysis and interpretation are much more powerful to help control the spread when that data is shared quickly and openly.

But it’s not all about producing new data when so much already exists. Analyzing data is hugely important. Sharing the results of this requires “showing your working”: the data you used, the methods you employed, and the software you used (with versions and parameters). This all takes time and effort, and bioinformaticians can help.

Roles of Bioinformatics

One of the main tools created by bioinformatics was databases. Several hundred databases hold different types of biological data like complete genomes and gene sequences. Databases allow the data to be stored and searched logically, enabling comparisons and links to be made that would have otherwise escaped the naked eye. These databases have increasing amounts of data that are growing at an exponential rate as we sequence more DNA.

Evolutionary relationships between organisms are examples of links that bioinformatics tools can make. When comparing genomes present in these databases, sequence similarity can be assessed. Increasing DNA sequence similarity is indicative of recent common ancestry. These tools allow us to build evolutionary trees and see how life relates to each other because knowing the basic mutation rate of DNA and how similar two sequences/genomes are, we can infer when two genetic sequences from different species diverged from a common ancestor.

Applications of bioinformatics in medicine

Bioinformatics has proven quite useful in medicine as the complete sequencing of the human genome has helped to unlock the genetic contribution for many diseases. Its applications include drug discovery, personalized medicine, preventative medicine, and gene therapy.

Drug discovery

Infectious diseases are currently the world’s major killer of children and young adults. According to WHO, infectious diseases account for over 13 million deaths yearly.

Developing countries record the most number of deaths from infectious diseases and this was contributed to the non-availability of drugs and the high cost associated with the drugs if available.

One of the main problems encountered is the development of cheap and efficient drugs for a disease that can be solved by rational drug design using Bioinformatics.

Furthermore, the pharmaceutical industry has moved from the trial and error process of drug discovery to a rational and structure-based drug design. With a successful and reliable drug design process, the time and cost of developing effective pharmacological agents can be reduced.

The process of drug target identification and drug candidate screening can be accelerated, and safer/more effective drugs can be developed based on molecular modeling and simulation.

Personalized medicine

Personalized medicine is a model of healthcare that is tailor-made to each person’s unique genetic make-up.

A patient’s genetic profile can assist the doctor to predict susceptibility to certain diseases, providing proper medication and with the proper dose to reduce side effects. It is applied in the treatment of personalized cancer medicine, diabetes-related diseases, and HIV.

Bioinformatics is used in personalized medicine to analyze data from genome sequencing or microarray gene expression analysis in search of mutations or gene variants that could affect a patient’s response to a particular drug or modify the disease prognosis.

Veterinary Sciences

The course of research in Veterinary Science has achieved an advanced level with the help of Bioinformatics. In this field, the application of Bioinformatics ranges specifically focuses on sequencing projects of animals including cows, pigs, and sheep. This has led to the development in overall production as well as the health of livestock. Moreover, Bioinformatics has helped scientists to discover new tools for the identification of vaccine targets.

Crop Improvement

Another important application of bioinformatics is in crop improvement. It makes effective usage of proteomic, metabolomic, genetic, and agricultural crop production to develop strong, more drought-resistant, and insect-resistant crops. Thereby enhancing the quality of livestock and making them disease resistant.

Preventive medicine

Preventive medicine focuses on the health of individuals, communities, and defined populations. It uses various research methods, including biostatistics, bioinformatics, and epidemiology, to understand the patterns and the causes of health and disease, and to transform such information into programs designed to prevent disease, disability, and death.

An example of preventive medicine is the screening of newborns immediately after birth for health disorders, such as genetic diseases or metabolic disorders, that are treatable but not clinically evident in the newborn period.

To develop such screening tests to identify the disease at an early stage, researchers use bioinformatic tools to analyze genomics, proteomics, and metabolomics data for possible disease biomarkers.

Waste Clean up

Another important application of bioinformatics is in waste clean-up. Here, the primary objective is to identify and assess the DNA sequencing of bacteria and microbes in order to use them for sewage cleaning, removing radioactive waste, clearing oil spills, etc. Did you know that as per the Guinness Book of world records, Bacterium Deinococcus Radiodurans is considered as the world’s toughest bacterium?

Microbial Genome

Microbial Genomes comprise of all the genetic material including chromosomal and extra-chromosomal components of bacteria and eukaryotes. And when it comes to the application of Bioinformatics, this is an important area. Apart from evaluating genome assembly, Bioinformatics tools also help in conducting DNA sequencing for application in areas including health and energy.

Evolutionary Studies

One of the great American scientists, Theodosius Dobzhansky rightly said, “Nothing in biology makes sense except in the light of evolution.” In order to understand biological problems and improve the quality of life, evolutionary studies play a decisive role. Through bioinformatics, one can compare the genomic data of different species and identify their families, functions, and characteristics

Some examples of Bioinformatics Tools:

BLAST:

BLAST ( Basic Local Alignment Search Tool) comes under the category of homology and similarity tools. It is a set of search programs designed for the Windows platform and is used to

perform fast similarity searches regardless of whether the query is for protein or DNA. A comparison of nucleotide sequences in a database can be performed. Also, a protein database can be searched to find a match against the queried protein sequence. NCBI has also introduced the new queuing system to BLAST (Q BLAST) that allows users to retrieve results at their convenience and format their results multiple times with different formatting options.

Depending on the type of sequences to compare, there are different programs:

• blastp compares an amino acid query sequence against a protein sequence database
• blastn compares a nucleotide query sequence against a nucleotide sequence database

FASTA:

FAST homology search A ll sequences. An alignment program for protein sequences was created by Pearson and Lipman in 1988. The program is one of the many heuristic algorithms proposed to speed up sequence comparison. The basic idea is to add a fast prescreen step to locate the highly matching segments between two sequences, and then extend these matching segments to local alignments using more rigorous algorithms such as Smith-Waterman.

EMBOSS:

EMBOSS (European Molecular Biology Open Software Suite) is a software-analysis package. It can work with data in a range of formats and also retrieve sequence data transparently from the Web. Extensive libraries are also provided with this package, allowing other scientists to release their software as open source. It provides a set of sequence-analysis programs and also supports all UNIX platforms.

Clustalw:

It is a fully automated sequence alignment tool for DNA and protein sequences. It returns the best match over a total length of input sequences, be it a protein or a nucleic acid.

RasMol:

It is a powerful research tool to display the structure of DNA, proteins, and smaller molecules. Protein Explorer, a derivative of RasMol, is an easier-to-use program.

PROSPECT:

PROSPECT (PROtein Structure Prediction and Evaluation Computer ToolKit) is a protein-structure prediction system that employs a computational technique called protein threading to construct a protein’s 3-D model.

PatternHunter:

PatternHunter, based on Java, can identify all approximate repeats in a complete genome in a short time using little memory on a desktop computer. Its features are its advanced patented algorithm and data structures, and the java language used to create it. The Java language version of PatternHunter is just 40 KB, only 1% the size of Blast while offering a large portion of its functionality.

Conclusion

In conclusion, the application of Bioinformatics is multi-fold and can be found in various domains! In a few years to come, bioinformatics shall be embedded in various fields.