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Full-Text Articles in Physical Sciences and Mathematics
System Designs To Perform Bioinformatics Sequence Alignment, Çağlar Yilmaz, Mustafa Gök
System Designs To Perform Bioinformatics Sequence Alignment, Çağlar Yilmaz, Mustafa Gök
Turkish Journal of Electrical Engineering and Computer Sciences
The emerging field of bioinformatics uses computing as a tool to understand biology. Biological data of organisms (nucleotide and amino acid sequences) are stored in databases that contain billions of records. In order to process the vast amount of data in a reasonable time, high-performance analysis systems are developed. The main operation shared by the analysis tools is the search for matching patterns between sequences of data (sequence alignment). In this paper, we present 2 systems that can perform pairwise and multiple sequence alignment operations. Through the optimized design methods, proposed systems achieve up to 3.6 times more performance compared …
An Automated Signal Alignment Algorithm Based On Dynamic Time Warping For Capillary Electrophoresis Data, Fethullah Karabi̇ber
An Automated Signal Alignment Algorithm Based On Dynamic Time Warping For Capillary Electrophoresis Data, Fethullah Karabi̇ber
Turkish Journal of Electrical Engineering and Computer Sciences
Correcting the retention time variation and measuring the similarity of time series is one of the most popular challenges in the area of analyzing capillary electrophoresis (CE) data. In this study, an automated signal alignment method is proposed by modifying the dynamic time warping (DTW) approach to align the time-series data. Preprocessing tools and further optimizations were developed to increase the performance of the algorithm. As a demonstrative case study, the developed algorithm is applied to the analysis of CE data from a selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) evaluation of the RNA secondary structure. The time-shift problem …