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In this paper we propose an on-the-fly reconfigurable hardware-software codesign based reconfigurable solution for real-time protein identification. Reconfigurable string matching is performed in the disciplines of protein identification and biomarkers discovery. With the generation of plethora of sequenced data and number of biomarkers for several diseases, it is becoming necessary to have an accelerated...
Deoxyribonucleic Acid (DNA) sequence alignment is essentially a way of comparing two or more DNA sequences with aim to find regions of similarities among them. The Smith-Waterman (SW) algorithm is a local alignment algorithm which is able to identify mutation in DNA sequences. However, the aforementioned algorithm tends to be slower in computation of long DNA sequences. Over decades ago, Field Programmable...
Computational Molecular Biology, Bioinformatics and Genomics are the most intriguing sciences to understand the human genome and diseases. These sciences use algorithms to analyze, and predict a hypothesis for the huge collected biological data in gene banks. Sequence alignment is the most important topics in bioinformatics which we are concerned with it in this paper. In comparison of bimolecular...
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...
Comparing three-dimensional structure of proteins is one of the most fundamental problems in bioinformatics. In recent years, various algorithms have been proposed to solve this problem efficiently. The proposed algorithms are very time-consuming due to high complexity and large input data. In this paper, hardware acceleration is applied to minimize the execution time of a previous algorithm, called...
The recent and astonishing accomplishments in the field of Genomics would not have been possible without the techniques, algorithms, and tools developed in Bioinformatics. Biological sequence comparison is an important operation in Bioinformatics because it is used to determine how similar two sequences are. As a result of this operation, one or more alignments are produced. DIALIGN is an exact algorithm...
The problem of longest common subsequence is defined as finding the longest subsequence common to two input sequences. It can be employed in many fields such as speech and signal processing, data compression, syntactic pattern recognition, string processing (bioinformatics), and genetic engineering. This paper describes the design of a parallel longest common protein subsequence hardware, implemented...
The paper deals with a very hot problem concerning computation biology - the searching for a given reference pattern within a very long DNA chain. The software solutions in the field are limited by amount of resources and processing times. That is why complex programmable devices are more and more commonly used in the applications concerning microbiology. The paper presents the approach which is a...
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