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FM-Index and Suffix Array are closely related to each other and are both extremely popular indexes for genomic sequences. They are used in several popular read alignment tools, including Bowtie, Bowtie 2, BWA, and GEM. In literature, there exist several Suffix Array Construction Algorithms (SACA). We have considered two popular SACA techniques: DivSufSort and SAIS. Both techniques construct suffix...
The emergence of bioinformatics has led to many new discoveries in living organisms. These discoveries would not have been possible without the developments made in the sequence alignment techniques. Many sequence alignment algorithms were developed to make the alignment process fast and accurate. However, the more precise algorithms take longer than their less precise counterparts. Researchers came...
In this paper, we develop an augmented reality sports broadcasting application for automatic detection, recognition of players during play, followed by display of personal information of players. The proposed application can be divided into four major steps. In first step, each player in the image is detected. In the second step, a face detection algorithm detects face of each player. In third step,...
The energy crisis is one of the major problems faced by Pakistan at the moment. It has adversely affected the industrial growth and restrained business nourishment which in turn has affected the overall economy of Pakistan. Proper energy saving measures need to be implemented in order to reduce the energy shortfall. The proper and efficient use of energy also helps in reducing different kinds of pollution...
DNA sequence alignment is a cardinal process in computational biology but also is much expensive computationally when performing through traditional computational platforms like CPU. Of many off the shelf platforms explored for speeding up the computation process, FPGA stands as the best candidate due to its performance per dollar spent and performance per watt. These two advantages make FPGA as the...
Smith-Waterman (S-W) algorithm is an optimal sequence alignment method and is widely used for genetic databases. This paper presents a Graphics Processing Units (CPUs) accelerated S-W implementation for protein sequence alignment. The paper proposes a new sequence database organization and several optimizations to reduce the number of memory accesses. The new implementation achieves a performance...
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