Improved Genome Annotation : Project
Initiative
With the increased number of whole genomes becoming available, automated tools for accurate and exhaustive identification of the genes and their associated function are becoming increasingly important. It is intended to develop such tools using a combination of computational and experimental methods. The Plasmodium falciparum (P. falciparum) genome has been chosen as the test-bed for this purpose. The choice of P. falciparum, the human malarial parasite, is dictated by two factors:
1) the availability of world class expertise on malarial biology in India and
2) the urgent need for a cure to malaria, which afflicts a considerable population both in India and elsewhere.
Out of an estimated 7000 genes, only 5300 genes have been identified. Although
complete sequences of all 14 chromosomes are available, one of the biggest
difficulties in assembling and annotating the genome has been its extremely
biased base composition. The unusually high (A+T) content (80.6%) is the cause
for the inability to achieve a successful assembly of the contigs into the
complete genome.
In view of these errors in the genome annotation of
P. falciparum it is necessary to improve the annotation and make it
available in a highly structured and computationally accessible form to
facilitate data exchange, comparison and analysis. A number of genes, which
are crucial for the survival of the parasite in humans, are yet to be
identified. This list of unidentified genes may contain putative drug
targets. One objective of the project is the identification of these regions
in the genome. A second objective is to improve the existing annotation.
Our efforts at improving the annotation involve the development of techniques for relating sequence to function in addition to the use of existing methods. The computational methods are being developed in concert with experimental approaches to verify the findings as well as guide the development of the computational algorithms. The improved annotation could help develop better drugs for combating malaria through identification of several new drug targets and an improved understanding of the biology of P.falciparum.
This project is being implemented through collaboration of different teams
from varied locations. These include:
* Tata Consultancy Services Ltd (TCS), Hyderabad
* Centre for DNA Finger-printing and Diagnostics (CDFD), Hyderabad
* Central Drug Research Institute (CDRI), Lucknow
* Institute of Genomics and Integrative Biology (IGIB), New Delhi
* Indian Institute of Science (IISc), Bangalore
* Indian Statistical Institute (ISI), Kolkata & New Delhi
* Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore
The team from TCS:
Dr. M. Vidyasagar
Dr. B. Gopalakrishnan
Dr. Sharmila Mande
Dr. Rajgopal Srinivasan
Dr. Sadhna Joshi, Aditya Rao, Siva Kumar Reddy
Sri Jyothsna Y, Raghavendra Gudladona, Monzoorul Haque
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