Volume 2, Issue 2, February 2012

A Tile-based Parallel Global Algorithm for Biological Sequence Alignment on multi core architecture [Download Paper]

D.D.Shrimankar and S.R.Sathe

Abstract—The Global algorithm is a compute-intensive based sequence alignment method. In this paper, we investigate extending several parallel methods, such as the wave-front methods for the Global algorithm, to achieve a significant speed-up on a multiple core. The simple parallel wave-front method can take advantage of the computing power of the multi-core processor but it cannot handle long sequences because of the physical main memory limit. On the other hand, the tiling method can process long sequences but with increased overhead due to the increased data transmission between main memory and secondary memory. To further improve the performance on multi-core processor, we propose a new tile-based parallel algorithm. We take advantage of the homological segments to divide long sequences into many short pieces and each piece pair (tile) can be fully held in the main memory. By reorganizing the main memory limitation instead of complete computed values only required values are stored in buffer and by using offset it is picked up when required. The experimental results show that our new tile-based parallel algorithm can outperform the simple parallel wave-front method. Especially for the long sequence alignment problem, the best performance of tile-based algorithm is on average about an order magnitude faster than the serial global algorithm.


Information & Communication Technology (ICT) for Agricultural Development in Rural Nigeria
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Emmanuel Ukpe and Jane Chukwurah

Abstract—Information & Communication Technology (ICT) has played a significant role in various sectors within the Nigerian Government. Its role to advance agricultural research, education and extension to improve the quality of life in a rural area is well established. Information Technology not only improves quality of life but can also help an average Nigerian farmer to get relevant information regarding crop production technologies, agro processing, market support, agro-finance and management of farm agri-business. Agriculture is the backbone of the rural community and modern farming practices and technologies has been implemented in many parts of the world which need to spread out to the areas unaffected by it; in this case, rural Nigeria. Both the communication networks and supporting infrastructure have to reach out to rural areas to allow the biggest entrepreneur community i.e., Farmers to deliver its best and thus create a stronger nation and economy. This paper discusses the main problems and possible solutions of the agricultural sector for the benefit of the rural dwellers of the country.