CAJ #6: Computational Genomics

Computers–what do they have to do with genetic engineering?
Well, sequencing the first human genome took an effort of almost ten years, but the introduction of advanced computer technology has enabled to complete a DNA sequence within just a couple of hours. This is achievable through Computational Genomics, also referred to as Computational Genetics, which is used to quickly analyze entire genome sequences of cells and organisms into a set of data. One example of this field is the HGP that could not have been completed in 2003 if it had not been for the developed, computational sequencing methods. Nowadays, there is no need for geneticists to spend endless days in laboratories using highly toxic and radioactive chemicals to sequence genomes, as it used to be the case around the 1970s. Computational genomics is one of the numerous sub fields of computational biology which has become an essential tool to biological discovery and “involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems” (Wikipedia). This computational science has been used to help create accurate models of the human brain, sequence genomes and much more. The sub field, in particular, focuses more on whole genomes, rather than on single genes, in order to have a better understanding of how the DNA of a living organism determines its biological function at the molecular level–and beyond. It is also intended to be used to sequence genomes of other types of life, such as animals and bacteria.

So, why computational genomics? Genomics are sequenced with computers and algorithms for the following reasons:

• reduction of the cost for detailing genomes; therefore, no need for additional experiments 
• detection of defects in DNA sequence
• fast location of genes by sorting through the genetic material
• identification and simplification of the information by implementation of mathematical algorithms and analysis 

A screenshot of a sequenced genome

Thanks to computational genomics, a great deal of base pairs and sequences have been able to be defined and registered online in the GenBank sequence database (=virtual collection of all available DNA sequences and their protein/base translations). Although considered highly unethical, it will be able to have several positive outcomes, such as:

• individualized healthcare; it could allow for doctors to prescribe medicine and treatments based on the patient’s pre-analyzed genetic patterns 
• finding new cures to rare diseases
• reducing the cost and time for genomic sequencing 

This field of science is, however, still ‘under construction’. There are several other research projects who are currently working on this area to come up with new numerical and computational approaches. But since computing plays a crucial role in the field of genomics, it is predicted that software and system improvements will soon be available.