What is Bioinformatics?
Bioinformatics can be referred to as the computational approaches of classifying, collecting, storing as well as analyzing various biochemical and biological information using computers. It is an interdisciplinary field that make uses of different methods and software tools in to order to understand biological data.
History of Bioinformatics
Paulien Hogeweg and Ben Hesper were the persons who coined the term bioinformatics in 1970 in order to refer to the study of various information processes in biotic system. The primary goal attached to bioinformatics is to increase the understanding of biological processes by applying intensive techniques to achieve a certain goal. Examples may include pattern recognition, machine learning algorithms etc.
Broad coverage of Bioinformatics
The coverage of bioinformatics includes various specialized areas of biology. Some of them are
- Functional genomics- It refers to as the process of identification of genes and the respective functions associated with them
- Structural genomics- This process includes the property of understanding different genomes structure of various species of organisms.
- DNA microarrays- In order to measure the level of gene expression in different tissues DNA microarrays are used. They also help in analyzing different forms of diseases in different stages of development.
- Medical informatics- It is basically a process of managing different biomedical data with special reference to biomolecules, in case of vitro assays as well as clinical trials.
Types of Bioinformatics
The process of bioinformatics includes different types of biological data. Some of them are as follows
- Structure of biological molecules
- Gene expression profiles
- Biochemical pathways
- Chromosomal mapping
- Phylogenic data
- Applications of bioinformatics
The field of bioinformatics is broad as well as multi-dimensional. Within the ambit of it lies, different fields into which bioinformatics can be applied. Some of them are as follows
- Drug Discovery- Bioinformatics is used in the field of bioinformatics in various ways. X ray crystallography as a drug discovery emerged more than 30 years ago. Within a short span of time, a significant change occurred in the structure of drug design. Through bioinformatics, the structure of targeted protein transformed into great design. This leads to chemical modification of molecular lead and gave optimized shape to the hydrogen bonds.
- Personalized medicine- With the advent of bioinformatics, the structure to personalized medicine has changed. Personalized medicine becomes a process of customization of healthcare with all the decisions being monitored to the individual patient with the use of genetic or other information. It also has helped in research of family of an individual patient considering family history, social circumstances as well as environment and behavior.
- Preventive medicine- The use of bioinformatics has also helped in the course of preventive medicine. Preventive medicine care usually consists of different measures taken to cure or prevent injuries or diseases.
- Therapy of Gene- It is a process of drug delivery basically including synthetic machinery of patient ‘s cell that acts as a therapeutic agent. The appropriate use of functional gene with a purpose to produce adequate amount of protein to correct some disorder permanently. The various strategies of gene therapy include removal of gene by antisense nucleotide or ribozymes, control of gene expression, addition of genes.
- Microbial Genome Applications- Through the process of bioinformatics various bacteria as well as microbes are identified that are helpful for cleaning waste. In the Guinness Book of World Records, Deinococcus radiodurans Bacteria is rated as the world’s toughest bacterium. The specification of this bacteria is that; it helps in repairing damaged DNA.
- Biotechnology- The wide concept of biotechnology includes different procedures for modifying living species in accordance with the human purposes. Improvement in the breeding programs is the first and foremost product of biotechnology. In the relevant field of bioinformatics, the concept of biotechnology has specifically identified organisms and microorganisms that can be very much useful in food manufacturers as well as dairy industry. One of such most important microorganism is Lactococcus lactis that is involved in the dairy industry.
- Agriculture- In case of agriculture the process of bioinformatics can be great help. In case of crop improvement information obtained from the model crop system suggested that data from the model crop system can be used in improvement of food crops. Examples of complete plant genomes are Arabidopsis thaliana (water cress) and Oryza sativa (rice).
- Insect resistance – With the help of biotechnology and through bioinformatics genes from bacillus thuringiensis have been discovered with the help of which serious pests have been successfully transferred to cotton, potatoes and maize. Through this new ability of the plants to resist insect attack the amount of insecticides being used for increasing the nutritional quality.
- Improve nutritional quality- in order to increase the level of vitamin A, scientists have recently succeeded in transferring structured genes into rice. A basic observation was found by the scientist was that when a gene from yeast was put inside a tomato it gave longevity of the fruit and got an extended shelf life. Presently tomatoes are plucked from the vine early in order to ensure they survive shipping without being rotten. The U.S Department of Agriculture hope that use of this technique can be applied to other fruits such as bell peppers, melons, strawberries etc. without being fearing for storage and complications.
- Varietal Information System- Bioinformatics can be of great help in case of developing varietal information system. In accordance with the Plant variety protection Act, terms like extant variety, candidate variety as well as farmer’s variety can be frequently used.
- Candidate variety is that kind of variety which needs to be registered under the plant protection act.
- Reference Variety is the variety which is included in the seed production chain including all released and notified extant varieties.
- Example variety consist of particular character that is used for comparison purpose.
- Farmers variety is that kind of variety which is solely developed for farmers which is also used for commercial cultivation for several years.
In order to use such information various ways can be put into use. Such as for varietal identification DUS testing is done.
- Plant genetic resource data base- In order to create a resource database for plants genetic, the concept of bioinformatics is of great help. Bioinformatics helps in handling the data of various locations for several years in a very systematic way. By providing the feature of addition, deletion as well as updating the information, bioinformatics helps in classification of PGR data based on various mentioned criteria. It also helps in retrieval of crucial data such as late maturity, dwarf types, biotic stresses, resistance to abiotic stresses etc. All such crucial data can be easily managed various computer aided programs and can be easily manipulated in different meaningful results.
- Biometrical Analysis- In case of crop improvement various biometrical analysis are being used. Some of the important biometrical analyses that are used in order to improve plant breeding as well as genetics are given as
- Various measures of variability such as standard deviation, mean, standard error, coefficient of variation etc.
- Correlation that includes phenotypic, genotypic as well as environmental correlations of simple, partial and multiple correlations.
- Path coefficients that includes analysis of phenotypic, genotypic and environmental paths.
- Discriminant function analysis
- D2 statistics with metroglyph analysis.
- Partial diallel, diallel as well as line x tester and triple test cross analysis.
- Generation mean analysis etc.
All such programs can be easily performed with the help of computer aided programs(CAD).
Pedigree analysis- Bioinformatics also helps in pedigree analysis of different cultivars and hybrids. Specific information about the parentage of cultivars as well as hybrids is entered into the memory of the computer that can be retrieved anytime later. The common lists of pedigree include hybrids that can be easily sorted out. It also helps in the pedigree analysis that can be used in planning plant breeding programs. Also the study of proteomics is of great help when it comes to pedigree analysis.
- Preparation of various reports – After getting the biometrical analysis of various data, results are interpreted on the basis of various reports and documents prepared. The reports can be of different kinds such
Bulletin and booklets
Research papers and articles
Such kinds of report can be easily documented through computers using simply MS word program. Also the editing and updating of the information can be done without putting extra reports.
- Diagrammatic representation – The various diagrams used through bioinformatics in case of inclusion of diagrams includes line diagrams, histograms, pie diagrams cluster diagram, path diagram etc. All such diagrams can be easily represented through computers using specific information.
- Planning of different breeding programs- It is a duty of the plan breeders to develop a plan program every year in order to make the breeding program successful. The following plan can be easily adopted using computers. Sowing plans for various breeding experimentation, crossing and selfing plans, Hybrid seed production plan as well as screening of plant breeding material against abiotic and biotic stresses, etc. are some of the important plants usually undertaken for different breeding programs.
Goals of Bioinformatics
The most important goal of bioinformatics is to develop efficient algorithms in order to measure various sequences. An algorithm called Needleman- Wunsch is a dynamic program that guarantees finding different optimal alignment of pairs of sequences. This algorithm can easily divide a large problem full of sequences into smaller sequence segments and can also help in setting up constructive solutions to different programs. Although the Needleman wunsch is taken to be productive and efficient, it is too slow for finding solutions for large sequence of databases. Therefore, it is required to give much attention to information based retrieval algorithms dealing with the huge amount of data. For example, BLAST (basic local alignment search tool).
While discussing all the relevant facts about bioinformatics, it has been observed that though bioinformatics is a useful tool for modern day database, it is also essential to keep a check on the drawbacks of it as well. More and more we go deeper in applications of it, we will be excelling over the loopholes making it a better and efficient technique to be used for future analysis.