Using Signal Processing to study DNA

SooryaKiran Bioinformatics was the brainchild of the first batch of students

of MPhil Bioinformatics, at Centre for Bioinformatics, University of Kerala,

Thiruvananthapuram. It developed its first tool for the US-based company called

Argus Biosciences, and was called GEN-SNiP. The software helps research students

and bioscientists to compare a regular sequence of DNAs to one which may be

deformed. It determines the Single Nucleotide Polymorphism (SNP) in a set of

mitochondrial DNA sequence against a reference DNA sequence. This is an

effective way of identifying genetic disorders since these disorders occur due

to changes in the protein structure which in turn makes up the DNA structure.

The tool compares the sequence to a regular sequence and identifies the

particular protein which has disturbed the chain. The tool is available online

at

www.argusbio.com/sooryakiran/gensnip/gensnip.php.

Dr. Achuthsankar S Nair, Director, Centre for Bioinformatics, is following a

vision to compress DNA. This will sound as a bizarre statement to a

biotechnologist or genetics professional, but he says he has a scientific logic

for this. “DNA is a language, just like any other computer language”, he said.

“Scientists have only researched on the biological nature of the DNA, but there

is so much information hidden in it as well. If we do some fundamental enquiries

on the informational nature of the DNA, there is so much each gene can tell us.

This information no doubt can be used to understand the DNA further, but it can

also be effectively used to compress the DNA, and when that happens, it will

simplify genetics to a great extent”, he explained.

Achuthsankar S Nair Professor, Centre for Bioinformatics, University of Kerala

As a first step towards this vision, he has incorporated the concept of

signal processing to molecular biology. At molecular level, the DNA comprises of

RNA, amino acids or proteins. Biologically, they form a chain in sequences of

various combinations of ACTG. If one were to consider that they convey data as

digital signals, it will enable scientists to identify a particular property of

the DNA. It will also identify where a particular gene, and will go a long way

in identifying deformities and differences from the reference structure. In

course of time, this institute also plans to extend signal processing to protein

sequences to address the diseases market. Since protein synthesis is the

backbone for study of diseases, signal processing of proteins will ensure that

one can identify 'hotspots' in proteins where irregularity is observed.