, SOAP: short oligonucleotide alignment program, Bioinformatics, vol.24, issue.5, 2008.
DOI : 10.1093/bioinformatics/btn025
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/24/5/713
, Zillions of Oligos Mapped, 2008.
, segemeh1 Read mapper using enhanced suffix array, with mismatch, insertion, deletion SA a SOAP2. Short Oligonucleotide Alignment program 2, 2008.
, Trie b SHRiMP. The SHort Read Mapping Pakage, 2009.
, Burrow-Wheeler Alignment tools (for short reads), 2009.
, [Technologies, ] commercial software, the free trial is avail- able
, 2012], the GPU version of BWA CUSHAW, p.2, 2012.
, GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors, Proceedings of the IEEE 13th International Conference on Computational Science and Engineering (CSE), pp.2-168, 2010.
, Efficient Hash Tables on the GPU, 2011.
, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-413, 1990.
DOI : 10.1016/S0022-2836(05)80360-2
, Opencl zone
, AMD Accelerated Parallel Processing, OpenCL Programming Guide, 2011.
, Evergreen Family Instruction Set Architecture Instructions and Microcode. Reference Guide, revision 1, 2011.
, OpenCL and the AMD APP SDK. online white paper , realesed by the AMD Staff, 2011.
, The landscape of parallel computing research: A view from berkeley, 2006.
, A view of the parallel computing landscape, Communications of the ACM, vol.52, issue.10, pp.5256-67, 2009.
DOI : 10.1145/1562764.1562783
, A new approach to text searching, SIGIR Forum, vol.23, pp.3-47, 1989.
, Unsupervised learning of multiple motifs in biopolymers using expectation maximization, Machine Learning, pp.51-80, 1993.
DOI : 10.1007/BF00993379
, Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp.28-36, 1994.
, Scratchpad memory, Proceedings of the tenth international symposium on Hardware/software codesign , CODES '02, pp.73-78, 2002.
DOI : 10.1145/774789.774805
, Evaluation of next-generation sequencing software in mapping and assembly, Journal of Human Genetics, vol.15, issue.6, pp.406-414, 2011.
DOI : 10.1038/jhg.2011.43
, Whole-genome re-sequencing, Current Opinion in Genetics & Development, vol.16, issue.6, pp.545-552, 2006.
DOI : 10.1016/j.gde.2006.10.009
, Protein alignment algorithms with an efficient backtracking routine on multiple GPUs, BMC Bioinformatics, vol.12, issue.1, p.181, 2011.
DOI : 10.1145/42411.42415
URL : http://doi.org/10.1186/1471-2105-12-181
, Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming, Bioinformatics, vol.27, issue.10, pp.271351-1358, 2011.
DOI : 10.1093/bioinformatics/btr151
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/27/10/1351
, Space/time trade-offs in hash coding with allowable errors, Communications of the ACM, vol.13, issue.7, pp.422-426, 1970.
DOI : 10.1145/362686.362692
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.20.2080
, The Direct3D 10 system, pp.724-734, 2006.
, Near-Optimal Space Perfect Hashing Algorithms, 2008.
, CMPH -C Minimal Perfect Hashing Library. online website, last updated, 2012.
, Bioinformatics Algorithms: Techniques and Applications, chapter A survey of seeding for sequence alignment, pp.126-152, 2008.
DOI : 10.1007/978-3-662-44753-6
, Brook for GPUs, ACM Transactions on Graphics, vol.23, issue.3, pp.777-786, 2004.
DOI : 10.1145/1015706.1015800
, Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Graphics Processing Unit Computing, 2010 Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology, pp.116-125, 2010.
DOI : 10.1109/PDMC-HiBi.2010.23
, A GPU Implementation of Fast Parallel Markov Clustering in Bioinformatics Using EllPACK-R Sparse Data Format, 2010 Second International Conference on Advances in Computing, Control, and Telecommunication Technologies, pp.173-175, 2010.
DOI : 10.1109/ACT.2010.10
, PASS: a program to align short sequences, Bioinformatics, vol.25, issue.7, pp.25967-968, 2009.
DOI : 10.1093/bioinformatics/btp087
, Universal classes of hash functions (Extended Abstract), Proceedings of the ninth annual ACM symposium on Theory of computing , STOC '77, pp.106-112, 1977.
DOI : 10.1145/800105.803400
, High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, issue.6, pp.1545-1556, 2011.
DOI : 10.1109/TCBB.2010.118
, Initial Experiences Porting a Bioinformatics Application to a Graphics Processor, Advances in Informatics, pp.415-425, 2005.
DOI : 10.1007/11573036_39
, An Exact Matching Approach for High Throughput Sequencing Based on BWT and GPUs, 2011 14th IEEE International Conference on Computational Science and Engineering, pp.173-180, 2011.
DOI : 10.1109/CSE.2011.41
, NextGenMap website of Center for Integrative Bioinformatics Vienna
, An optimal algorithm for generating minimal perfect hash functions, Information Processing Letters, vol.43, issue.5, pp.43257-264, 1992.
DOI : 10.1016/0020-0190(92)90220-P
, A model of evolutionary change in proteins, Atlas of Protein Sequence and Structure, vol.5, issue.3, pp.345-352, 1978.
, Alignment of whole genomes, Nucleic Acids Research, vol.27, issue.11, pp.272369-2376, 1999.
DOI : 10.1093/nar/27.11.2369
, Fast algorithms for large-scale genome alignment and comparison, Nucleic Acids Research, vol.30, issue.11, pp.302478-2483, 2002.
DOI : 10.1093/nar/30.11.2478
URL : http://doi.org/10.1093/nar/30.11.2478
, Highly efficient mapping of the Smith-Waterman algorithm on CUDA-compatible GPUs, ASAP 2010, 21st IEEE International Conference on Application-specific Systems, Architectures and Processors, pp.29-36, 2010.
DOI : 10.1109/ASAP.2010.5540796
, Biological sequence analysis: Probabilistic models of proteins and nucleic acids, 1998.
DOI : 10.1017/CBO9780511790492
, CUSA and CUDE: GPU-Accelerated Methods for Estimating Solvent Accessible Surface Area and Desolvation, Journal of Computational Biology, vol.16, issue.4, pp.523-537, 2009.
DOI : 10.1089/cmb.2008.0157
, MOM: maximum oligonucleotide mapping, Bioinformatics, vol.25, issue.7, pp.25969-970, 2009.
DOI : 10.1093/bioinformatics/btp092
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/25/7/969
, Advantages and GPU implementation of high-performance indexed DNA search based on suffix arrays, High Performance Computing and Simulation (HPCS), 2011 International Conference on, pp.49-55, 2011.
, An efficient algorithm for large-scale detection of protein families, Nucleic Acids Research, vol.30, issue.7, pp.1575-1584, 2002.
DOI : 10.1093/nar/30.7.1575
, Parallelized agent-based simulation on CPU and graphics hardware for spatial and stochastic models in biology, Proceedings of the 9th International Conference on Computational Methods in Systems Biology, CMSB '11, pp.73-82, 2011.
DOI : 10.1145/2037509.2037521
, An algorithm for fast edit distance computation on GPUs, 2012 Innovative Parallel Computing (InPar), 2012.
DOI : 10.1109/InPar.2012.6339593
, Striped Smith-Waterman speeds database searches six times over other SIMD implementations, Bioinformatics, vol.23, issue.2, pp.156-161, 2007.
DOI : 10.1093/bioinformatics/btl582
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/23/2/156
, PHYLIP (Phylogeny Inference Package) Version 3.5c, 2010.
, Opportunistic data structures with applications, Proceedings 41st Annual Symposium on Foundations of Computer Science, pp.390-398, 2000.
DOI : 10.1109/SFCS.2000.892127
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.23.7615
, Accelerating molecular dynamic simulation on graphics processing units, Journal of Computational Chemistry, vol.66, issue.6, pp.30864-872, 2009.
DOI : 10.1002/jcc.21209
, Accelerating HMMER on GPUs by implementing hybrid data and task parallelism, Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, BCB '10, pp.418-421, 2010.
DOI : 10.1145/1854776.1854844
, Heterogeneous Computing with OpenCL, 2011.
, Parallel position weight matrices algorithms, Parallel Computing, issue.8, p.37, 2010.
DOI : 10.1016/j.parco.2010.10.001
URL : https://hal.archives-ouvertes.fr/hal-00623404
, Twin peaks, Proceedings of the 19th international conference on Parallel architectures and compilation techniques, PACT '10, pp.205-216, 2010.
DOI : 10.1145/1854273.1854302
, Improving CUDASW++, a Parallelization of Smith-Waterman for CUDA Enabled Devices, 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum, pp.490-501, 2011.
DOI : 10.1109/IPDPS.2011.182
, DOPA: GPU-based protein alignment using database and memory access optimizations, BMC Research Notes, vol.4, issue.1, p.261, 2011.
DOI : 10.1093/bioinformatics/btl582
URL : http://doi.org/10.1186/1756-0500-4-261
, GPU-accelerated protein sequence alignment, 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp.2442-2446, 2011.
DOI : 10.1109/IEMBS.2011.6090679
, Graphs, hypergraphs and hashing, Proceedings of the 19th International Workshop on Graph-Theoretic Concepts in Computer Science, WG '93, pp.153-165, 1994.
DOI : 10.1007/3-540-57899-4_49
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.456.142
, Amino acid substitution matrices from protein blocks., Proceedings of the National Academy of Sciences, vol.89, issue.22, pp.10915-10919, 1992.
DOI : 10.1073/pnas.89.22.10915
, Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures, PLoS Computational Biology, vol.12, issue.9, p.1000502, 2009.
DOI : 10.1371/journal.pcbi.1000502.t001
, Bit Parallelism - NFA Simulation, Revised Papers from the 6th International Conference on Implementation and Application of Automata, CIAA '01, pp.149-160, 2002.
DOI : 10.1007/3-540-36390-4_13
, BFAST: An Alignment Tool for Large Scale Genome Resequencing Clawhmmer: A streaming hmmer-search implementation, SC, p.11, 2005.
, Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing, Briefings in Bioinformatics, vol.11, issue.2, pp.181-197, 2010.
DOI : 10.1093/bib/bbp046
, GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition, BMC Research Notes, vol.4, issue.1, p.97, 2011.
DOI : 10.1186/1756-0500-4-97
, OpenCL -The open standard for parallel programming of heterogeneous systems
, Accelerating Protein Sequence Alignment, ACM Trans. Reconfigurable Technol. Syst, vol.19, issue.2, pp.1-9
, Exploiting Memory Access Patterns to Improve Memory Performance in Data-Parallel Architectures, IEEE Transactions on Parallel and Distributed Systems, vol.22, issue.1, pp.105-118, 2011.
DOI : 10.1109/TPDS.2010.107
, Algorithm alley: Hash functions. Dr. Dobb's, Journal of Software Tools, vol.22, issue.9, 1997.
, SeqMap: mapping massive amount of oligonucleotides to the genome, Bioinformatics, vol.24, issue.20, pp.242395-2396, 2008.
DOI : 10.1093/bioinformatics/btn429
, Accelerating genomewide association studies using cuda compatible graphics processing units, Bioinformatics, Systems Biology and Intelligent Computing IJCBS '09. International Joint Conference on, pp.70-76, 2009.
DOI : 10.1109/ijcbs.2009.32
, BLAT---The BLAST-Like Alignment Tool, Genome Research, vol.12, issue.4, pp.656-664, 2002.
DOI : 10.1101/gr.229202
, OpenCL -The open standard for parallel programming of heterogeneous systems, 2008.
, BarraCUDA - a fast short read sequence aligner using graphics processing units, BMC Research Notes, vol.5, issue.1, p.27, 2012.
DOI : 10.1093/bioinformatics/btn032
URL : http://doi.org/10.1186/1756-0500-5-27
, Versatile and open software for comparing large genomes, Genome Biology, vol.5, issue.R12, 2004.
, cugwam: Genome-wide association multifactor dimensionality reduction using cuda-enabled high-performance graphics processing unit, 2010 IEEE International Conference on, pp.336-340, 2010.
DOI : 10.1109/bibmw.2010.5703824
, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012.
DOI : 10.1093/bioinformatics/btp352
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381
, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology, vol.10, issue.3, 2009.
DOI : 10.1186/gb-2009-10-3-r25
, Reconfigurable Computing, chapter Bioinformatics Applications, 2005.
, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.251954-1960, 2009.
DOI : 10.1093/bioinformatics/btp324
, Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, vol.26, issue.5, pp.589-595, 2010.
DOI : 10.1093/bioinformatics/btp698
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828108
, A survey of sequence alignment algorithms for next-generation sequencing, Briefings in Bioinformatics, vol.11, issue.5, pp.473-483, 2010.
DOI : 10.1093/bib/bbq015
, A fast CUDA implementation of agrep algorithm for approximate nucleotide sequence matching, 2011 IEEE 9th Symposium on Application Specific Processors (SASP), pp.74-77, 2011.
DOI : 10.1109/SASP.2011.5941082
, Mapping short DNA sequencing reads and calling variants using mapping quality scores, Genome Research, vol.18, issue.11, pp.1851-1858, 2008.
DOI : 10.1101/gr.078212.108
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577856
, SOAP: short oligonucleotide alignment program, Bioinformatics, vol.24, issue.5, pp.24713-714, 2008.
DOI : 10.1093/bioinformatics/btn025
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/24/5/713
, SOAP2: an improved ultrafast tool for short read alignment, Bioinformatics, vol.25, issue.15, pp.251966-1967, 2009.
DOI : 10.1093/bioinformatics/btp336
, An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases, 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009.
DOI : 10.1109/IPDPS.2009.5160931
, ZOOM! Zillions of oligos mapped, Bioinformatics, vol.24, issue.21, pp.242431-2437, 2008.
DOI : 10.1093/bioinformatics/btn416
, Bloom Filter Performance on Graphics Engines, Parallel Processing (ICPP), 2011 International Conference on, pp.522-531, 2011.
, NVIDIA Tesla: A Unified Graphics and Computing Architecture, IEEE Micro, vol.28, issue.2, pp.39-55, 2008.
DOI : 10.1109/MM.2008.31
, Design and implementation of a CUDA-compatible GPU-based core for gapped BLAST algorithm, Procedia Computer Science, vol.1, issue.1, pp.495-504, 2010.
DOI : 10.1016/j.procs.2010.04.053
, High performance Intra-task parallelization of Multiple Sequence Alignments on CUDA-compatible GPUs, 2011 NASA/ESA Conference on Adaptive Hardware and Systems (AHS), pp.360-366, 2011.
DOI : 10.1109/AHS.2011.5963959
, A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs, 2009 IEEE 7th Symposium on Application Specific Processors, pp.94-100, 2009.
DOI : 10.1109/SASP.2009.5226343
, Improved tools for biological sequence comparison, Proc. Natl Acad. Sci. USA, pp.852444-2448, 1988.
, Linear hashing: a new tool for file and table addressing, Proceedings of the sixth international conference on Very Large Data Bases, pp.212-223, 1980.
, CUDA-BLASTP on Tesla GPUs, 2010.
, Mapping of BLASTP Algorithm onto GPU Clusters, 2011 IEEE 17th International Conference on Parallel and Distributed Systems, pp.236-243, 2011.
DOI : 10.1109/ICPADS.2011.79
, CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, pp.1678-1684, 2011.
, GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment, IEEE International Conference on High Performance Computing, pp.363-374, 2006.
DOI : 10.1007/11945918_37
, Biosequence database scanning on a GPU, Parallel and Distributed Processing Symposium, p.8, 2006.
, CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units, BMC Research Notes, vol.2, issue.1, p.73, 2009.
DOI : 10.1186/1756-0500-2-73
URL : http://doi.org/10.1186/1756-0500-2-73
, Long read alignment based on maximal exact match seeds, Bioinformatics, vol.28, issue.18, pp.28-318, 2012.
DOI : 10.1093/bioinformatics/bts414
, CUDA???MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units, Pattern Recognition Letters, vol.31, issue.14, pp.312170-2177, 2010.
DOI : 10.1016/j.patrec.2009.10.009
, MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA, Application-specific Systems, Architectures and Processors 20th IEEE International Conference on, pp.121-128, 2009.
, Parallel reconstruction of neighborjoining trees for large multiple sequence alignments using cuda, IEEE International Workshop on High Performance Computational Biology, 2009.
, CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions, BMC Research Notes, vol.3, issue.1, p.93, 2010.
DOI : 10.1186/1756-0500-3-93
, An Ultrafast Scalable Many-Core Motif Discovery Algorithm for Multiple GPUs, 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum, pp.428-434, 2011.
DOI : 10.1109/IPDPS.2011.183
, DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI, BMC Bioinformatics, vol.12, issue.1, 2011.
DOI : 10.1186/gb-2009-10-3-r25
URL : http://doi.org/10.1186/1471-2105-12-85
, CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform, Bioinformatics, vol.28, issue.14, 2012.
DOI : 10.1093/bioinformatics/bts276
, Batch Records Insertion into Multidimensional Linear Dynamic Hashing Table on GPU, Journal of Computational Information Systems, vol.8, issue.10, pp.4293-4301, 2012.
, PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, pp.440-445, 2002.
DOI : 10.1093/bioinformatics/18.3.440
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.147.8001
, GPU-Euler: Sequence Assembly Using GPGPU, 2011 IEEE International Conference on High Performance Computing and Communications, pp.153-160, 2011.
DOI : 10.1109/HPCC.2011.29
, A Family of Perfect Hashing Methods, The Computer Journal, vol.39, issue.6, pp.39547-554, 1996.
DOI : 10.1093/comjnl/39.6.547
, CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment, BMC Bioinformatics, vol.9, issue.Suppl 2, p.10, 2008.
DOI : 10.1186/1471-2105-9-S2-S10
, Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, Journal of Molecular Biology, vol.288, issue.5, pp.911-940, 1999.
DOI : 10.1006/jmbi.1999.2700
, Cramming More Components Onto Integrated Circuits, Proceedings of the IEEE, vol.86, issue.1, p.38, 1965.
DOI : 10.1109/JPROC.1998.658762
, Progress in digital integrated electronics, Technical Digest 1975. International Electron Devices Meeting, pp.11-13, 1975.
, Design and implementation of the Smith-Waterman algorithm on the CUDA-compatible GPU, 2008 8th IEEE International Conference on BioInformatics and BioEngineering, pp.1-6, 2008.
DOI : 10.1109/BIBE.2008.4696721
, Flexible Pattern Matching in Strings ? Practical on-line search algorithms for texts and biological sequences, 2002.
, A general method applicable to the seach for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, issue.3, pp.48433-453, 1970.
, Parallel computing for intensive comparison of genomic sequences, 2008.
URL : https://hal.archives-ouvertes.fr/tel-00435792
, Speeding up subset seed algorithm for intensive protein sequence comparison, 2008 IEEE International Conference on Research, Innovation and Vision for the Future in Computing and Communication Technologies, 2008.
DOI : 10.1109/RIVF.2008.4586333
URL : https://hal.archives-ouvertes.fr/inria-00321457
, PLAST: parallel local alignment search tool for database comparison, BMC Bioinformatics, vol.10, issue.1, p.329, 2009.
DOI : 10.1186/1471-2105-10-329
URL : https://hal.archives-ouvertes.fr/inria-00425301
, SSAHA: A Fast Search Method for Large DNA Databases, Genome Research, vol.11, issue.10, pp.1725-1729, 2001.
DOI : 10.1101/gr.194201
, Algorithms for Loop Matchings, SIAM Journal on Applied Mathematics, vol.35, issue.1, pp.68-82, 1978.
DOI : 10.1137/0135006
, NVIDIA GF100, World's fastest GPU delivering great gaming performance with true geometric system
, NVIDIA's Next Generation CUDA Compute Architecture: Fermi. white paper, version 1
, Introduction and Overview. version 1
, NVIDIA OpenCL best practice guide, 2009.
, MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison, Protein Science, vol.301, issue.11, pp.112606-2621, 2002.
DOI : 10.1110/ps.0215902
, Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score, BMC Bioinformatics, vol.9, issue.1, p.531, 2008.
DOI : 10.1186/1471-2105-9-531
, Accelerating large-scale protein structure alignments with graphics processing units, BMC Research Notes, vol.5, issue.1, p.116, 2012.
DOI : 10.1186/1471-2105-8-425
URL : http://doi.org/10.1186/1756-0500-5-116
, Optimal neighborhood indexing for protein similarity search, BMC Bioinformatics, vol.9, issue.1, 2008.
DOI : 10.1186/1471-2105-9-534
URL : https://hal.archives-ouvertes.fr/inria-00340510
, A new approach to fragment assembly in DNA sequencing, Proceedings of the fifth annual international conference on Computational biology , RECOMB '01, pp.256-267, 2001.
DOI : 10.1145/369133.369230
, Implementation of Smith-Waterman Algorithm in OpenCL for GPUs, 2010 Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology, pp.48-56, 2010.
DOI : 10.1109/PDMC-HiBi.2010.16
, Ultra-fast FFT protein docking on graphics processors, Bioinformatics, issue.19, pp.262398-2405, 2010.
DOI : 10.1093/bioinformatics/btq444
URL : https://hal.archives-ouvertes.fr/inria-00537988
, mpscan: Fast Localisation of Multiple Reads in Genomes, Proc. 9th Workshop on Algorithms in Bioinformatics, pp.246-260, 2009.
DOI : 10.1016/j.jcss.2007.10.001
URL : https://hal.archives-ouvertes.fr/lirmm-00407173
, GPU accelerated RNA folding algorithm, Using Emerging Parallel Architectures for Computational Science / International Conference on Computational Science, 2009.
DOI : 10.1016/b978-0-12-384988-5.00014-0
URL : https://hal.archives-ouvertes.fr/hal-00637827
, GASSST: global alignment short sequence search tool, Bioinformatics, vol.26, issue.20, pp.262534-2540, 1920.
DOI : 10.1093/bioinformatics/btq485
URL : https://hal.archives-ouvertes.fr/hal-00531499
, Long time-scale simulations of in vivo diffusion using GPU hardware, 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009.
DOI : 10.1109/IPDPS.2009.5160930
, SHRiMP: Accurate Mapping of Short Color-space Reads, PLoS Computational Biology, vol.8, issue.5, p.1000386, 2009.
DOI : 10.1371/journal.pcbi.1000386.t004
, Highthroughput sequence alignment using Graphics Processing Units, BMC Bioinformatics, 2007.
DOI : 10.1186/1471-2105-8-474
URL : http://doi.org/10.1186/1471-2105-8-474
, Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis, Journal of Computational Biology, vol.19, issue.6, pp.796-813, 2012.
DOI : 10.1089/cmb.2012.0022
, Inside Intel Nehalem Microarchitecture, NOTUR 2009, The 8th Annual Meeting on High Performance Computing and Infrastructure in Norway, 2009.
, Accelerating Error Correction in High-Throughput Short-Read DNA Sequencing Data with CUDA, IEEE International Workshop on High Performance Computational Biology, 2009.
, Quality-score guided error correction for short-read sequencing data using CUDA, Procedia Computer Science, vol.1, issue.1, pp.1129-1138, 2010.
DOI : 10.1016/j.procs.2010.04.125
, The Exact Online String Matching Problem: a Review of the Most Recent Results, ACM Computing Surveys, vol.45, issue.2, 2013.
, Accelerating global sequence alignment using CUDA compatible multi-core GPU, 2010 Fifth International Conference on Information and Automation for Sustainability, pp.201-206, 2010.
DOI : 10.1109/ICIAFS.2010.5715660
, Using quality scores and longer reads improves accuracy of Solexa read mapping, BMC Bioinformatics, vol.9, issue.1, 2008.
DOI : 10.1186/1471-2105-9-128
, Identification of common molecular subsequences, Journal of Molecular Biology, vol.147, issue.1, pp.195-197, 1981.
DOI : 10.1016/0022-2836(81)90087-5
, An Efficient Program for Phylogenetic Inference Using Simulated Annealing, 19th IEEE International Parallel and Distributed Processing Symposium, pp.198-200, 2005.
DOI : 10.1109/IPDPS.2005.90
, RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees, Bioinformatics, vol.21, issue.4, pp.456-463, 2005.
DOI : 10.1093/bioinformatics/bti191
, Versatile and declarative dynamic programming using pair algebras, BMC Bioinformatics, vol.6, issue.1, 2005.
, GPU Parallelization of Algebraic Dynamic Programming, Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 09, 2009.
DOI : 10.1007/978-3-642-14403-5_31
URL : https://hal.archives-ouvertes.fr/inria-00438219
, Fast and accurate protein substructure searching with simulated annealing and GPUs, BMC Bioinformatics, vol.11, issue.1, p.446, 2010.
DOI : 10.1186/1471-2105-11-446
, Sequence alignment with GPU: Performance and design challenges, 2009 IEEE International Symposium on Parallel & Distributed Processing, pp.1-10, 2009.
DOI : 10.1109/IPDPS.2009.5161066
, Many-core algorithms for statistical phylogenetics, Bioinformatics, vol.25, issue.11, pp.251370-1376, 2009.
DOI : 10.1093/bioinformatics/btp244
, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673
, Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.9, issue.4, p.99, 2012.
DOI : 10.1109/TCBB.2012.49
, Bit-Parallel Multiple Pattern Matching, Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference, 2011.
DOI : 10.1007/978-3-642-31500-8_30
URL : https://hal.archives-ouvertes.fr/inria-00637227
, Graph Clustering Via a Discrete Uncoupling Process, SIAM Journal on Matrix Analysis and Applications, vol.30, issue.1, pp.121-141, 2008.
DOI : 10.1137/040608635
, Manycore highperformance computing in bioinformatics, Advances in Genomic Sequence Analysis and Pattern Discovery, p.page chapter, 2011.
, GPU-BLAST: using graphics processors to accelerate protein sequence alignment, Bioinformatics, vol.27, issue.2, pp.182-188, 2011.
DOI : 10.1093/bioinformatics/btq644
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018811
, Evaluating the use of GPUs in liver image segmentation and HMMER database searches, 2009 IEEE International Symposium on Parallel & Distributed Processing, pp.1-12, 2009.
DOI : 10.1109/IPDPS.2009.5161073
, Short read DNA fragment anchoring algorithm, BMC Bioinformatics, vol.10, issue.Suppl 1, p.10, 2009.
DOI : 10.1186/1471-2105-10-S1-S17
URL : http://doi.org/10.1186/1471-2105-10-s1-s17
, Linear pattern matching algorithms, 14th Annual Symposium on Switching and Automata Theory (swat 1973), pp.1-11, 1973.
DOI : 10.1109/SWAT.1973.13
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.474.9582
, Agrep -a fast approximate pattern-matching tool, Proc. of USENIX Technical Conference, pp.153-162, 1992.
, Fast text searching: allowing errors, Communications of the ACM, vol.35, issue.10, pp.83-91, 1992.
DOI : 10.1145/135239.135244
, Architecture comparisons between Nvidia and ATI GPUs: Computation parallelism and data communications, 2011 IEEE International Symposium on Workload Characterization (IISWC), 2011.
DOI : 10.1109/IISWC.2011.6114180
, TM-align: a protein structure alignment algorithm based on the TM-score, Nucleic Acids Research, vol.33, issue.7, pp.2302-2309, 2005.
DOI : 10.1093/nar/gki524
, Accelerating Biological Sequence Alignment Algorithm on GPU with CUDA, 2011 International Conference on Computational and Information Sciences, pp.18-21, 2011.
DOI : 10.1109/ICCIS.2011.61
, The time complexity, the number of uint operations and the memory access number of a, p.79