Automatic Parallelization for Parallel Architectures Using Smith Waterman Algorithm-Literature Review
Ananth Prabhu G, Ganesh Aithal · 2014
This paper presents a literature survey conducted for research oriented developments made till. The significance of this paper would be to provide a deep rooted understanding and knowledge transfer regarding existing approaches for gene sequencing and alignments using Smith Waterman algorithms and their respective strengths and weaknesses. In order to develop or perform any quality research it is always advised to conduct research goal oriented literature survey that could facilitate an in depth understanding of research work and an objective can be formulated on the basis of gaps existing between present requirements and existing approaches. Gene sequencing problems are one of the predominant issues for researchers to come up with optimized system model that could facilitate optimum processing and efficiency without introducing overheads in terms of memory and time. This research is oriented towards developing such kind of system while taking into consideration of dynamic programming approach called Smith Waterman algorithm in its enhanced form decorated with other supporting and optimized techniques. This paper provides an introduction oriented knowledge transfer so as to provide a brief introduction of research domain, research gap and motivations, objective formulated and proposed systems to accomplish ultimate objectives. Keywords: Smith-Waterman (SW), Multiple-Instruction, Multiple-Data (MIMD), Single Instruction, Multiple Data (SIMD), Smith-Waterman algorithm (SW), Diagonal Parallel Sequencing and Alignment Approach (DPSAA).