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In this article, we will discuss what is bioinformatics in detail. We will especially discuss the benefits of using databases that provide information about nucleotide sequences of genes and genomes, and amino acid sequences of proteins and protein structures.
Bioinformatics refers to the interdisciplinary field that combines biology, mathematics, informatics, computer science, and statistics. In this field, biological data is analyzed and interpreted for different uses. Some biologists consider bioinformatics as a computational branch of biology which solves specific biological problems.
Types of Biological Experiments
Biological experiments are of two types:
- In-vivo: It is inside the living organism
- In-vitro: It is inside the glass or a test tube
Bioinformatics makes a third type of analysis possible that employs computers and silicon chips. This is referred to as in-silico biology.
What is Bioinformatics?
Different technologies, for instance, gene sequencing and microarrays are employed for the analysis of genes and proteins nowadays. These technologies generate a huge amount of data which ranges from the sequences of genomes to the structure and function of proteins. Bioinformatics helps to analyze this enormous amount of data. Hence, we can define bioinformatics like this:
"An interdisciplinary science (that incorporates biology with statistics and computer science) that involves the collection, organization, manipulation, analysis, and storage of biological data is known as bioinformatics"
Databases in Bioinformatics
Information regarding gene sequences to amino acid sequences of proteins results in the creation of large databases. Databases play a fundamental role in bioinformatics applications. They have different kinds of data like empirical and predicted data that can be either general or specific to a certain organism. The structure and function of these databases differ greatly. These databases can be accessed online and analysis can be done on the selected data. Because this data requires access and search, hence the software developer plays a fundamental role in doing so. A few examples of databases that exist today are:
- The European Molecular Biology Laboratory – Nucleotide sequence database
- Protein Data Bank at Europe – Protein sequence searches
- ArrayExpress – a microarray database with the level and types of mRNA expressed in various cells
- BLAST stands for Basic Local Alignment Search Tool. Researchers use it to find similarities between sequences they are studying with those already present in the database
After sequencing the genome, scientists use bioinformatics to make compare that genome with that of other organisms by using the available databases. It can assist in finding the degree of similarity between organisms which then indicates how closely organisms are related and if there are organisms that can be employed in experiments as a model for humans. For instance, the fruit fly Drosophila.
An animal Caenorhabditis elegans has been employed as a model organism to study the genetics of organ development, neuron development, and cell death. It was the first organism whose genome was fully sequenced. Because it has less than 1000 cells only, hence its model was quite useful.
Applications of Bioinformatics
One of the applications of bioinformatics involves using databases with the Plasmodium genome to detect the genes or proteins that can be modified or influenced to control the parasite. For example, creating a vaccine for malaria.
Importance of Bioinformatics
The use of bioinformatics in biology dates back to the time when Frederick Sanger determined the insulin sequence. After that, multiple scientists developed novel tools and techniques to analyze and sequence DNA. Today, we have an evolved form of bioinformatics which is a critical part of research in many areas of biology. The importance of bioinformatics can be established from the points mentioned below:
- Bioinformatics helps in genes sequencing and plays a fundamental role in gene expression
- It enables to mine text of biological literature
- It plays a crucial role in analyzing the protein expression
- It helps to compare and interpret sequences
- Structural bioinformatics aids in the modeling of various molecules like DNA, RNA, and proteins
- It helps to organize and analyze the biological pathways
Objectives of Bioinformatics
The fundamental objective of bioinformatics is to comprehend biological processes with enhanced speed and efficiency. It involves developing and implementing different intensive computational methods to manage biological information along with developing new algorithms to find relationships among large data sets.
Some of the vital methods in bioinformatics include:
- Pattern recognition
- Data mining
- Signal processing
- Visualization
- Machine learning
The methods discussed above assist in sequence analysis, sequence alignment, drug discovery, function prediction, drug design, gene finding, genome assembly, protein structure, DNA mapping, 3-D creation and visualization of protein models, etc.
Remember that bioinformatics and biological computation are slightly different from each other. This is because bioinformatics employs computation for an efficient comprehension of biological data. On the other hand, biological computation is employed to build biological computers through the use of bioengineering.
Software and Tools
Besides databases as discussed above, many other tools and software are available for bioinformatics too. These tools include:
- Simple command-line tools
- Open-source software
- Web services in bioinformatics
- Bioinformatics workflow management systems
- BioCompute objects
Open-source bioinformatics software
Many open-source software are available freely which assist the researchers in bioinformatics. The researchers are more excited than ever because of new and emerging algorithms, the potential for in-silico experiments, and other attributes these tools offer. The primary benefit of using open-source tools is the support of the community and the creation of new plug-ins for different purposes.
Some common bioinformatics software are listed below:
- Bioconductor
- UGENE
- BioPerl
- BioPython
- Apache Taverna
- BioJava, EMBOSS
Open Bioinformatics Foundation is a non-profit organization that provides support to make software and tools better.
Web services in bioinformatics
Scientists have developed REST and SOAP-based interfaces that enable to use and transfer the bioinformatics data around the globe. It enables the researcher to work without stressing about the maintenance of software and database. Bioinformatics services if of the following three types:
- Sequence search services (SSS)
- Multiple sequence alignment (MSA)
- Biological sequence analysis (BSA)
Bioinformatics workflow management systems
A wide range of critical tasks is executed by the bioinformatics workflow management system. One of the critical qualities of this kind of system is that the scientists have access to an easy-to-use system that enables them to create custom workflows. Moreover, sharing the workflow between the scientists and researchers becomes easier. It also offers interactive tools for the scientists and allows them to track the results and create workflow steps.
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