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Communications of the ACM
Bioinformatics
Scalable Parallel Programming with CUDA
Queue - GPU Computing
Bioinformatics
ZOOM! Zillions of oligos mapped
Bioinformatics
Bioinformatics
Sequence alignment with GPU: Performance and design challenges
IPDPS '09 Proceedings of the 2009 IEEE International Symposium on Parallel&Distributed Processing
Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA
IPDPS '09 Proceedings of the 2009 IEEE International Symposium on Parallel&Distributed Processing
MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA
ASAP '09 Proceedings of the 2009 20th IEEE International Conference on Application-specific Systems, Architectures and Processors
Optimizing data intensive GPGPU computations for DNA sequence alignment
Parallel Computing
CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences
Proceedings of the 15th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming
Acceleration of the Smith-Waterman algorithm using single and multiple graphics processors
Journal of Computational Physics
FANGS: high speed sequence mapping for next generation sequencers
Proceedings of the 2010 ACM Symposium on Applied Computing
Pattern Recognition Letters
GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors
CSE '10 Proceedings of the 2010 13th IEEE International Conference on Computational Science and Engineering
Some computer organizations and their effectiveness
IEEE Transactions on Computers
CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
BIBMW '09 Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshop
Smith-Waterman Alignment of Huge Sequences with GPU in Linear Space
IPDPS '11 Proceedings of the 2011 IEEE International Parallel & Distributed Processing Symposium
A fast CUDA implementation of agrep algorithm for approximate nucleotide sequence matching
SASP '11 Proceedings of the 2011 IEEE 9th Symposium on Application Specific Processors
An Exact Matching Approach for High Throughput Sequencing Based on BWT and GPUs
CSE '11 Proceedings of the 2011 14th IEEE International Conference on Computational Science and Engineering
RECONFIG '11 Proceedings of the 2011 International Conference on Reconfigurable Computing and FPGAs
Mapping of BLASTP Algorithm onto GPU Clusters
ICPADS '11 Proceedings of the 2011 IEEE 17th International Conference on Parallel and Distributed Systems
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After the reference genomes of many organisms are sequenced in the post-genetic era, an important issue is to do the re-sequencing of individual genomes with high-throughput reads. Many next-generation sequencing machines have been proposed in the last few years and a series of re-sequencing tools have been developed for mapping short reads to the reference genome. FRESCO is a frequency-based re-sequencing tool without using hash look-up table algorithm and Burrows-Wheeler transformation. FRESCO offers more flexibility in the mapping and then obtains satisfactory mapping results. However, FRESCO is a computation-intensive tool. Therefore, in this paper, a tool, CUDA-FRESCO v1.0, was proposed to reduce the computation time of FRESCO by using the graphics processing units with CUDA. By comparing to FRESCO, CUDA-FRESCO v1.0 achieved 63× speedups for the mapping kernel and 20× speedups for the overall computation time.