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Posted by:
Ranjith Vasireddy
Article
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What is Bioinformatics?
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What is Bioinformatics?
by: Ranjith Vasireddy, M.Tech (CSE), IIT Kanpur, UP.
Motivation
Biological data are being produced at an exponential rate. For eg. GeneBank repository of nucleic acid sequences contained more than 11,546,000 entries and the SWISS-PROT database of protein sequences contained more than 95,320 entries. These databases are doubling in size every 12 months.
Strong mathematical and automated tools are necessary for processing these large amount of data. When ever there is a large amount of data, computer scientist can automate the processing of it / learning (using machine learing principles) from the data. Since the data is experimental, there is a lot of noise part also involved in the data (for eg. Gene Expression Data). Sophisticated mathematical methods to minimise the noise in this experimental data and to process data is also a major requirement.
How much should a non-biologist know in Biology to work in Bio-informatics?
Understanding Biology is necessary to work in bioinformatics. But the question of how much to understand depends on the area in Biology in which you work. Let me justify my statement like this. We shall take to examples to justify my statement.
1)Every DNA sequence consists of exons and introns. Scientists still donot know the funcions of introns. They are considered to be the part of a junk DNA (ofcourse some researchers contradict it). One problem in this area is like this: Given a DNA fragment, identify whether it is a exon or intron. There are several methods to do it. But we can automate this by applying machine learning techniques. For someone who wants to apply ML techniques for this problem, it is sufficient to understand DNA as a language like this:
DNA is a string formed from the language with an alphabet set {A, C, G, T}.
RNA is a a string formed from the language with an alphabet set {A, C, G, U}.
Similary proteins are string formed from the alphabet set having 20 amino acids as alphabets.
2) One shld not take it granted that minimal knowledge in biology is enough to work in bioinformatics. Let me tell you one more research area where you need lot of biological background. For eg. one wants to understand the bio-chemical path ways that govern regulatory signals in an organism. One can apply mathematical models or control system theories. To build any model, he/she should master the underlying theory (here biochemical path way). How the biochemical pathway works? What exactly is bio-chemical pathway? To what depth should one work (phosphorylation, oxidation also should be included?).
How much biology is required and necessary depends on the problem domain that one is working on, in the area of bioinformatics or/and computational biology.
A primer on essential biology
Cells are the fundamental working units of every living system. All the instructions needed to direct their activities are contained within the chemical DNA (deoxyribonucleic acid). DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the "particular" side-by-side arrangement of bases along the DNA strand (eg. CTTGAAACCTG). The order spells out the exact instructions required to create a particular organism with its own unique traits. The Genome is an organism s complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism contains about 5,80,000 DNA base pairs, while human and mouse genomes have some 3 billion. Although genes get a lot of attention, it s the Proteins that [perform most life fuctions and even make up the majority of cellular structures. Proteins are large, complex molecules made up of smaller subunits called amino acids. Chemical properties that distinguish the 20 different amino acids cause the protein chains to fold up into specific 3D sturcutures that define their particular functions in the cell.
Defining Bioinformatics
Even though there is no clear definition for bioinformatics, I consider bioinformatics as the following: "Bioinformatics is applying informatics techniques (derived from disciplienes such as theoretical/applied mathematics, computer science and statistics) to understand, to analyse, to organize and to produce some biologically relevant results from biological data".
As stated by M. Gerstein, analysis in Bioinformatics predominantly focus on three type of large datasets available in molecular biology: macromolecular structures, genome sequences, and the results of functional genomic experiments (eg expression data). Bioinformatics employs a wide range of computational tehcniques including sequence and structural alignment, database design and data mining, macromolecular geometry, phylogenetic tree construction, prediction of protein structure and function, gene fining and expression data clustering. There are several applications in this area like finding homologues, designing drugs and so on.
Note:
1. I m using Bioinformatics and Computational Biology interchangeably in this article, even though there is a lot of blurred difference between them.
2. I m not an expert in Bio-informatics. So please take every thing in this article with a pinch of salt.
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The Existence of Cells