The Infona portal uses cookies, i.e. strings of text saved by a browser on the user's device. The portal can access those files and use them to remember the user's data, such as their chosen settings (screen view, interface language, etc.), or their login data. By using the Infona portal the user accepts automatic saving and using this information for portal operation purposes. More information on the subject can be found in the Privacy Policy and Terms of Service. By closing this window the user confirms that they have read the information on cookie usage, and they accept the privacy policy and the way cookies are used by the portal. You can change the cookie settings in your browser.
Sequence alignment is a core step in the processing of DNA and RNA sequencing data. In this paper, we present a high performance GPU accelerated set of APIs (GASAL) for pairwise sequence alignment of DNA and RNA sequences. The GASAL APIs provide accelerated kernels for local, global as well as semi-global alignment, allowing the computation of the alignment score, and optionally the start and end...
We propose a novel FPGA-accelerated BWA-MEM implementation, a popular tool for genomic data mapping. The performance and power-efficiency of the FPGA implementation on the single Xilinx Virtex-7 Alpha Data add-in card is compared against a software-only baseline system. By offloading the Seed Extension phase onto the FPGA, a two-fold speedup in overall application-level performance is achieved and...
The fast decrease in cost of DNA sequencing has resulted in an enormous growth in available genome data, and hence led to an increasing demand for fast DNA analysis algorithms used for diagnostics of genetic disorders, such as cancer. One of the most computationally intensive steps in the analysis is represented by the DNA read alignment. In this paper, we present an accelerated version of BWA-MEM,...
We present the first accelerated implementation of BWA-MEM, a popular genome sequence alignment algorithm widely used in next generation sequencing genomics pipelines. The Smith-Waterman-like sequence alignment kernel requires a significant portion of overall execution time. We propose and evaluate a number of FPGA-based systolic array architectures, presenting optimizations generally applicable to...
Multicore architectures, especially hardware accelerator systems with heterogeneous processing elements, are being increasingly used due to the increasing processing demand of modern digital systems. However, data communication in multicore architectures is one of the main performance bottle-necks. Therefore, reducing data communication overhead is an important method to improve the speed-up of such...
The Smith-Waterman (SW) algorithm is one of the widely used algorithms for sequence alignment in computational biology. With the growing size of the sequence database, there is always a need for even faster implementation of SW. In this paper, we have implemented two Recursive Variable Expansion (RVE) based techniques, which are proved to give better speedup than any best dataflow approach at the...
Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.