By Shahbaz Alam and Dr. Sylvia Mitchell, ContributorsWHAT IS BIOINFORMATICS?
THE HUMAN genome project, completed in 2001, sequenced the entire human genome. Once researchers realised how much data was being generated from the knowledge gained from the human genome project, they began to use the computer to help keep track and analyse all this genetic information. These computer methods and databases have become more sophisticated and the new field of bioinformatics was born.
Bioinformatics refers to the development and use of computer tools for managing, retrieving, analysing and integrating sequences and other data from biological systems. In the new, post-genomic era, many researchers and biotech companies no longer study genes or proteins one by one, as had traditionally been done. The new paradigm calls for a highly-automated endeavour operating on a massive scale.
High-throughput, increasingly sensitive techniques, the integration of multiple techniques into a single platform, robotics and computers are taking the place of lab technicians. Without computers to keep track of everything, this approach would be impossible. The field has exploded. In the 30 years from 1966 to 1995, a Medline (Internet) search on the term bioinformatics turns up just 38 papers. However, between 1998 and 2002, over 1,700 papers were published. Gene banks now contain more than 10 billion nucleotides of nucleic acid sequence data and doubles in size every year.
DETERMINING FUNCTIONS
OF HUMAN GENE
Before its completion, the Human Genome Project was often portrayed as an end in itself. Researchers now recognise that gene sequences are only a starting point. The next step is to establish what those genes and their protein products actually do, as well as when they do it and why. For instance, is a particular disease caused by a gene that is not activated at the right time or by a protein that that does not fold properly or by the disruption of a cell-signalling pathway? It turns out that determining what individual genes and their protein products actually do is no simple task.
There are a lot of genes in a human cell (over 30,000). From here it gets even more complicated. There are more unique proteins than there are genes, with some experts estimating that the total number of proteins could be as high as a million or more. Most of the proteins that make a cell work are modified after their original amino acid building blocks have been assembled, when sugar groups and phosphate groups are added. Such post-translational modifications as these are not revealed by the DNA sequence for a particular protein.
An example of the potential of bioinformatics is in the pharmaceutical industry. The development of a single drug costs an average of US$500 million. Bioinformatics speeds up results by using combinatorial chemistry and proteomics to produce more than one million potential drug targets per year. Sorting out the complicated molecular pathways is possible using bioinformatics. If even two or three targets yield marketable drugs, it will be worthwhile.
MORE DATA TO COME
Even more data will come from new technologies for assaying gene expression patterns, protein structure and protein-protein interactions. Handling this data, making sense of it, and making all this data accessible will be the challenge for bioinformatics researchers. Current computers and bioinformatics software are good but not good enough. The challenge of this new approach to biology is that it is so complex that it will require computers that are larger and faster than anything currently available.
New, more powerful software, and algorithms are also desperately needed. The computer industry is already working on supercomputers that are 500 times more powerful and 40 times faster than anything now on the market. Bioinformatics will have numerous uses, among them proteomics and genomics, drug development, clinical medicine, bioarcheology, anthropology, evolutionary biology, DNA forensics (identification), agriculture, livestock breeding and bioprocessing.
In conclusion, bioinformatics will draw professionals from various disciplines. From the physical sciences, biosciences, biostatics and information technology to meet the future challenges of bioinformatics. Here in Jamaica, there is an incipient bioinformatics capability that is being nurtured at the University of the West Indies and will produce results that will affect how biotechnology is performed in the future.
Shahbaz Alam is a lecturer in the Department of Mathematics and Computer Science, and Dr. Sylvia Mitchell is an assistant lecturer at the Biotechnology Centre, University of the West Indies, Mona, St. Andrew.
