ESTexplorer: EST analysis for Parasitic Nematodes

Inbiosis seminar on 13 Feb 2009 presented by Prof. Dr. Shoba Ranganathan from Macquaie University, Australia.

After a brief introduction on parasitic nematodes, Prof. Shoba described the problem she and her team encountered during EST analysis. None of the softwares available such as ESTannotator, ESTAP, PartiGene, and EGassembler provides the workflow they need. This is how they started developing a semi-automated pipeline called ESTexplorer to handle larget EST datasets. This pipeline has embedded EST pre-processing, clustering, assembly, database similarity searches and most importantly functional annotation. Click here to view this paper.

Furthermore, ESTexplorer can perform GO and pathway mapping, which can predict how the gene is involved in a biochemical/biological pathway. Her team has successfully identified several genes in parasitic nematodes that can be potentially used as new drug target. I have some EST data for GenBank submission that could really use a pipeline like this. Too bad I missed the workshop.

Besides showing interest in a wide variety of subjects, Prof. Shoba is the current editor of BMC bioinformatics. She can be easily described as a very busy person spending 80 working hours per week. Don’t be shocked because she considers “thinking of work” as working. But how many of us actually work 55 hours a week? Count me out.

Lastly, she did not forget to invite our participation in The International Conference on Bioinformatics (InCoB) which will be held in Singapore in later this year. Check out my previous post for more details.