Bioinformatics FAQ (Frequently Asked Questions) - What is bioinformatics

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(Continued from previous part...)

They can be mapped---that is, their sequences can be parsed to find sites where so-called "restriction enzymes" will cut them.

They can be compared, usually by aligning corresponding segments and looking for matching and mismatching letters in their sequences. Genes or proteins that are sufficiently similar are likely to be related and are therefore said to be "homologous" to each other---the whole truth is rather more complicated than this. Such cousins are called "homologues".

If a homologue (a related molecule) exists, then a newly discovered protein may be modelled---that is the three dimensional structure of the gene product can be predicted without doing laboratory experiments.

Bioinformatics is used in primer design. Primers are short sequences needed to make many copies of (amplify) a piece of DNA as used in PCR (the Polymerase Chain Reaction).

Bioinformatics is used to attempt to predict the function of actual gene products.

Information about the similarity, and, by implication, the relatedness of proteins is used to trace the "family trees" of different molecules through evolutionary time.

There are various other applications of computer analysis to sequence data, but, with so much raw data being generated by the Human Genome Project and other initiatives in biology, computers are presently essential for many biologists just to manage their day-to-day results

Molecular modelling / structural biology is a growing field which can be considered part of bioinformatics. There are, for example, tools which allow you (often via the Net) to make pretty good predictions of the secondary structure of proteins arising from a given amino acid sequence, often based on known "solved" structures and other sequenced molecules acquired by structural biologists.

Structural biologists use "bioinformatics" to handle the vast and complex data from X-ray crystallography, nuclear magnetic resonance (NMR) and electron microscopy investigations and create the 3-D models of molecules that seem to be everywhere in the media.

note

Unfortunately the word "map" is used in several different ways in biology/genetics/bioinformatics. The definition given above is the one most frequently used in this context, but a gene can be said to be "mapped" when its parent chromosome has been identified, when its physical or genetic distance from other genes is established and---less frequently---when the structure and locations of its various coding components (its "exons") are established.

What is Bioinformatics?---The Loose definition

There are other fields---for example medical imaging / image analysis which might be considered part of bioinformatics. There is also a whole other discipline of biologically-inspired computation; genetic algorithms, AI, neural networks. Often these areas interact in strange ways. Neural networks, inspired by crude models of the functioning of nerve cells in the brain, are used in a program called PHD to predict, surprisingly accurately, the secondary structures of proteins from their primary sequences.

What almost all bioinformatics has in common is the processing of large amounts of biologically-derived information, whether DNA sequences or breast X-rays.

How old is the discipline?

"How old is bioinformatics?" The answer to this one depends on which source you choose to read.

From T K Attwood and D J Parry-Smith's "Introduction to Bioinformatics", Prentice-Hall 1999 [Longman Higher Education; ISBN 0582327881]:

"The term bioinformatics is used to encompass almost all computer applications in biological sciences, but was originally coined in the mid-1980s for the analysis of biological sequence data."

From Mark S. Boguski's article in the "Trends Guide to Bioinformatics" Elsevier, Trends Supplement 1998 p1:

"The term "bioinformatics" is a relatively recent invention, not appearing in the literature until 1991 and then only in the context of the emergence of electronic publishing...

"...However, some of my role models when I was a graduate student (Margaret O. Dayhoff, Russell F. Doolittle, Walter M. Fitch and Andrew D. McLachlan) had been building databases, developing algorithms and making biological discoveries by sequence analysis since the 1960s---long before anyone thought to label this activity with a special term (if anything it was called `molecular evolution'). Even a relatively new kid on the block, the National Center for Biotechnology Information (NCBI), is celebrating its 10th anniversary this year, having been written into existence by US Congressman Claude Pepper and President Ronald Reagan in 1988. So bioinformatics has, in fact, been in existence for more than 30 years and is now middle-aged."

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