Scalable multicore architectures for long DNA sequence comparison

Sánchez, Friman; Cabarcas, Felipe; Ramírez, Alex; Valero, Mateo

doi:10.1002/cpe.1753

Cited by 3 publications

(2 citation statements)

References 17 publications

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“…We complement those experiments by looking at a different problem: the multiple sequence alignment with ClustalW [90]. Our results show that although ClustalW-PW also tolerates high memory latencies (similar to the observations in [75,82,83]), the bandwidth requirements are quite different. Moreover, we study a manycore based on ASIC accelerators while previous work [75] used ASIPs instead.…”

Section: Clustalw Implementationsmentioning

confidence: 52%

Multicore Architectures

2010

Chapman &Amp; Hall/CRC Computational Science

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Section: Clustalw Implementationsmentioning

confidence: 52%

Multicore Architectures

2010

Chapman &Amp; Hall/CRC Computational Science

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“…Biological sequence comparison is one of the most important tasks in bioinformatics. In the paper Scalable multicore architectures for long DNA sequence comparison , Friman Sánchez from the Technical University of Catalonia and Felipe Cabarcas, Alex Ramirez, and Mateo Valero from the Barcelona Supercomputing Center, Spain, propose two implementations of the Smith–Waterman algorithm in the IBM Cell/BE architecture: one centralized and one distributed. The centralized approach uses the shared memory for communication and the distributed approach uses local buffers and a delayed synchronization protocol.…”

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confidence: 99%

Special Issue: Euro‐Par 2010

Bougé

Lengauer

2011

Concurrency and Computation

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This special issue of Concurrency and Computation: Practice and Experience contains revised and extended versions of selected papers presented at the Euro-Par 2010 conference.Euro-Par-the European Conference on Parallel Computing-is an annual series of international conferences dedicated to the promotion and the advancement of all aspects of parallel and distributed computing. Euro-Par covers a wide spectrum of topics from algorithms and theory to software technology and hardware-related issues, with application areas ranging from scientific to mobile and cloud computing. The main audience of Euro-Par are the researchers in academic institutions, government laboratories, and industrial organizations.Euro-Par 2010, the 16th conference in the Euro-Par series, was organized by the Institute for High Performance Computing and Networking of the Italian National Research Council and was held at the Hotel Continental Terme on the Italian island of Ischia, in the Naples Bay.Fourteen broad topics were defined and advertised, covering a large variety of aspects of parallel and distributed computing. The call for papers attracted a total of 256 submissions. The submitted papers were reviewed at least three and, in many cases, four times. A total of 90 papers were finally accepted for publication. This makes a global acceptance rate of 35%. The authors of the accepted papers come from 24 countries, with the four main contributing countries-USA, France, Spain, and Germany-accounting for about 55% of the authors. The distribution of authors followed the pattern typical for a Euro-Par conference: of the 10 authors, this year, six have been academic researchers, three PhD students, and one from industry.The topical distribution of the papers in the proceedings of Euro-Par 2010 reflects the current trends in the field of parallel and distributed computing: 18 of 90 papers are devoted to the relatively new topic Multicore and Manycore Programming. This figure was 11 in 2009 and was even lower in 2008 when the subject was part of the topic High-Performance Architectures and Compilers. On the other hand, the well-established Euro-Par topics such as Support Tools and Environments or Scheduling and Load-Balancing, for instance, have remained quite stable throughout the years. These figures demonstrate that the topic structure of Euro-Par has the flexibility to adapt to current trends in a wide spectrum of research areas.With its topic structure, Euro-Par has been filling two complementary rôles: as a regular meeting place for established communities and as a place to develop new communities. In recent years, the latter rôle has been strengthened by the introduction of satellite workshops, at which researchers can meet initially and form a new community that later settles and flourishes in other fora. In 2010, the number of satellite workshops was higher than ever before, 11, and we strive to have it grow further, maintaining the Euro-Par claim of being the wide-spectrum conference on parallelism in Europe.Returning to the spread of p...

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Parallel Optimal Pairwise Biological Sequence Comparison

2016

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Many bioinformatics applications, such as the optimal pairwise biological sequence comparison, demand a great quantity of computing resource, thus are excellent candidates to run in high-performance computing (HPC) platforms. In the last two decades, a large number of HPC-based solutions were proposed for this problem that run in different platforms, targeting different types of comparisons with slightly different algorithms and making the comparative analysis of these approaches very difficult. This article proposes a classification of parallel optimal pairwise sequence comparison solutions, in order to highlight their main characteristics in a unified way. We then discuss several HPC-based solutions, including clusters of multicores and accelerators such as Cell Broadband Engines (CellBEs), Field-Programmable Gate Arrays (FPGAs), Graphics Processing Units (GPUs) and Intel Xeon Phi, as well as hybrid solutions, which combine two or more platforms, providing the actual landscape of the main proposals in this area. Finally, we present open questions and perspectives in this research field.

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Scalable multicore architectures for long DNA sequence comparison

Cited by 3 publications

References 17 publications

Multicore Architectures

Multicore Architectures

Special Issue: Euro‐Par 2010

Parallel Optimal Pairwise Biological Sequence Comparison

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