Super-computing cluster, Bio-chrome for sequencing of large genomes.

                                          

Giving new dimensions to the sequencing of hundreds of genomes or biological data of human beings, the Centre for Development of Advanced Computing (C-DAC) has developed a supercomputing cluster called asBiochrome. It is an advanced blade server-based high performance computing (HPC) facility that has a computing capacity of 5 teraflop, said director general of C-DAC RajatMoona.
He was speaking to media persons on the eve of launch of the machine on Tuesday at Accelerating Biology 2012, the three-day symposium at a hotel in city.

He said, “The computing facility is one of the technology enablers that can accelerate the process of analysing, data mining and simulation of biological data. The advent of next generation sequencing technology has brought in a new dimension to understanding the molecular basis for the occurrence of diseases.’’

The pace of sequencing is leading to data overload and the ability to analyse is much beyond the existing computing capabilities. In order to gear up to tackle these challenges, most biologists are adopting the use of cyber infrastructure. Bioinformatics Resources and Applications Facility (BRAF) at C-DAC is an effort towards providing high-end supercomputing facility to researchers working in the area of life sciences.

The project is funded by the department of information technology, ministry of communications and information technology.

C-DAC is collaborating with organisations like National Cancer Institute (NCI) of USA, Tata Memorial Centre (Mumbai), Roslin Institute (UK), University of Edinburgh (UK), University of Surrey (UK), Oregon Health and Science University (USA), Sanger Institute (UK), National Centre for Cell Science (Pune) and University of Pune (Pune).

Building a more stable genome

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  Researchers at the Genome Institute of Singapore (GIS) have, for the very first time, developed a computational tool that comes with a guarantee on its reliability when reconstructing the DNA sequence of organisms, thus enabling a more streamlined process for reconstructing and studying genomic sequences.
 
The work, lead by Dr Niranjan Nagarajan, Assistant Director of Computational and Mathematical Biology at the GIS, was reported in the November 2011 issue of the Journal of Computational Biology.
 
The genomic study of life (plants and animals alike) is based on computational tools that can first piece together the DNA sequence of these organisms, a process called genome assembly, that is similar to solving a giant puzzle or putting together the words in a book from a shredded copy. Due to the sheer scale of this challenge, existing approaches for genome assembly rely on heuristics and often result in incorrect reconstructions of the genome. The work reported here represents the first algorithmic solution for genome assembly that provides a quality guarantee and scales to large datasets. A new and improved implementation for this algorithm called Opera is now freely available at http://sourceforge.net/projects/operasf/ and has been used at the GIS for successfully assembling large plant and animal genomes.
 
The assembled genome of an organism forms the basis for a range of downstream biological investigations and serves as a critical resource for the research community. The draft human genome, for example, was obtained at the expense of billions of dollars, serves as a fundamental resource for biomedical research and is, in fact, still being refined. Improved assembly tools thus serve to generate the most complete and accurate draft genomes that can be reconstructed from the data, avoiding mis-assembly related dead-ends for downstream research as well as minimizing the painstaking effort needed to refine and correct a draft assembly.
 
“Genetic studies of organisms of interest for human health (such as those causing infectious diseases), agriculture, animal husbandry and other areas of the bio-economy, such as biofuels, are driven by the availability of draft genome sequences, said Dr Nagarajan. “This research describes a novel computational approach to reconstruct more complete and accurate draft genomes. From an algorithmic perspective, Opera demonstrates the utility of a clear optimization function and an exact algorithm derived from a parametric complexity analysis in providing a robust solution to a seemingly intractable problem.”
 Mihai Pop, Associate Prof, Department of Computer Science; and Interim Director, Center for Bioinformatics and Computational Biology at the University of Maryland said: “Opera is an important advance in genome assembly algorithms – currently it is the best stand-alone genome scaffolder available in the community. In Opera, Dr Nagarajan's team has introduced a rigorous theoretical framework for genome scaffolding as well as a practical implementation that achieves remarkable performance. These results are impressive given the substantial research in the field over the past 30 years, as well as the numerous developments spurred in recent years by advances in sequencing technologies.”                                                                                                                      

India joins 16 nations to crack wheat genome in three years

 

The elusive wheat genome - the most important crop globally - will be cracked within the next three years. Indian scientists have joined 16 other nations - the US, the UK, France, Italy, Switzerland, Germany, Czech Republic, Norway, Israel, Turkey, Russia, China, Japan, Australia and Argentina - in the initiative.

The department of biotechnology (DBT) has sanctioned about Rs 34 crore for over four years to three institutes - Punjab Agriculture University, ICAR and Delhi University - for the project.

Prof Nagendra Kumar Singh from ICAR's National Research Center on Plant Biotechnology in New Delhi said, "The project is likely to be completed in five years. But, we will crack the code within three years."

Wheat has 21 chromosomes of which one will be decoded by the 21 Indian scientists. The wheat genome is 42 times bigger than rice genome.

" India had bumper wheat production of 84 million tons this year. Once we have cracked its genetic code, we can develop disease-resistant wheat faster. Brown and yellow rust diseases are a big threat to wheat," Prof Singh said.
 

On Wednesday, 31 Indian scientists also cracked the genetic code of arhar ( pigeonpea or red gram), the second most important pulse crop of India. This is the first plant genome sequenced indigenously. Now, this will help faster development of high yielding, disease and insect-resistant varieties of arhar for higher productivity and lower prices of pulses. 

The scientists have identified 47,004 protein coding genes in the arhar genome, of which 1,213 genes are for disease resistance and 152 genes for tolerance to drought, heat and salinity that make it a hardy crop. 

Asha, the genome of popular arhar variety, was assembled using long sequence reads of 454-FLX second generation sequencing technology resulting in 511 million base pairs of high quality genome sequence information.