Scientific Computing: Bioinformatics and Computational Biology

Bioinformatics is an interdisciplinary field with biology, computer science, statistics and information technology at its core.

A colossal amount of data is generated by biological experiments. When biologists need tools to analyse, store and interpret this data, Bioinformatics comes for the rescue. The job of a bioinformatician entails writing algorithms, creating user interface, creating databases and help molecular biologists in interpreting the computed data.

Nussinov's Algorithm - Traceback Step

In my basic and advanced courses of bioinformatics, we were taught about dynamic programming algorithms, namely, Nussinov’s algorithm for RNA secondary structure prediction, Viterbi algorithm for Decoding of HMM and UPGMA for phylogenetic tree construction. Though these algorithms are accurate, they are very slow for large data sets. Heuristic algorithms were used instead of dynamic programming algorithms as they gave approximate but fast solutions.

Protein Structure

There are tons of algorithms to solve any problem in any other field. However, it is extremely difficult to solve a biology problem because, the living system is so complex and divergent. It becomes almost impossible to device a perfect algorithm. For example, finding the actual representation of the protein structure and all its function is one of the biggest challenges faced by bioinformaticians today.

A myriad of packages for predicting genes (Ex: GenScan), for aligning sequences (Ex: BLAST, CLUSTALW and CLUSTAL Omega), constructing phylogenetic trees are available, but none of these give an accurate solution for all types of problems. Though researchers are facing new problems every day, they are being helped immensely by computer scientists. It will certainly take a number of years to solve complicated problems, but we must remain dedicated to this field since it offers great hope in solving diseases like HIV, Cancer, Alzheimer’s etc that plague the society today.

References:

Dr. Sami Khuri – Bioinformatics CS123A and CS223

http://iase-web.org/documents/papers/icots7/5D2_ARHI.pdf