Bioinformatics FAQ (Frequently Asked Questions) - What is bioinformatics

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What is Pharmacogenomics?

Pharmacogenomics is the application of genomic approaches and technologies to the identification of drug targets. Examples include trawling entire genomes for potential receptors by bioinformatics means, or by investigating patterns of gene expression in both pathogens and hosts during infection, or by examining the characteristic expression patterns found in tumours or patients samples for diagnostic purposes (possibly in the pursuit of potential cancer therapy targets).

The term "pharmacogenomics" is used for the more "trivial"---but arguably more useful---application of bioinformatics approaches to the cataloguing and processing of information relating to pharmacology and genetics, for example the accumulation of information in databases like this one. (Thanks to Ivanovi.)

What is Pharmacogenetics?

All individuals respond differently to drug treatments; some positively, others with little obvious change in their conditions and yet others with side effects or allergic reactions. Much of this variation is known to have a genetic basis. Pharmacogenetics is a subset of pharmacogenomics which uses genomic/bioinformatic methods to identify genomic correlates, for example SNPs (Single Nucleotide Polymorphisms), characteristic of particular patient response profiles and use those markers to inform the administration and development of therapies. Strikingly, such approaches have been used to "resurrect" drugs thought previously to be ineffective, but subsequently found to work with in subset of patients. They can also be used for optimizing the doses of chemotherapy for particular patients.

Overview of most common bioinformatics programs

Everyday bioinformatics is done with sequence search programs like BLAST, sequence analysis programs, like the EMBOSS and Staden packages, structure prediction programs like THREADER or PHD or molecular imaging/modelling programs like RasMol and WHATIF.

Overview of most common bioinformatics technology

Currently, a lot of bioinformatics work is concerned with the technology of databases (Thanks again to Ivanovi.) These databases include both "public" repositories of gene data like GenBank or the Protein DataBank (the PDB), and private databases, like those used by research groups involved in gene mapping projects or those held by biotech companies. Making such databases accessible via open standards is very important. Consumers of bioinformatics data use a range of computer platforms: from the more powerful and forbidding UNIX boxes favoured by the developers and curators to the far friendlier Macs often found populating the labs of computer-wary biologists.

Databases of existing sequencing data can be used to identify homologues of new molecules that have been amplified and sequenced in the lab. The property of sharing a common ancestor, homology, can be a very powerful indicator in bioinformatics (see below).

Acquisition of sequence data

Bioinformatics tools can be used to obtain sequences of genes or proteins of interest, either from material obtained, labelled, prepared and examined in electric fields by individual researchers/groups or from repositories of sequences from previously investigated material.

Analysis of data

Both types of sequence can then be analysed in many ways with bioinformatics tools.

They can be assembled. Note that this is one of the occasions when the meaning of a biological term differs markedly from a computational one (see the amusing confusion over the issue at Web-based geek forum Slashdot). Computer scientists, banish from your mind any thought of assembly language. Sequencing can only be performed for relatively short stretches of a biomolecule and finished sequences are therefore prepared by arranging overlapping "reads" of monomers (single beads on a molecular chain) into a single continuous passage of "code". This is the bioinformatic sense of assembly.

(Continued on next part...)

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