Bioinformatics challenges of new sequencing technology, Trends in Genetics, vol.24, issue.3, pp.142-149, 2008. ,
DOI : 10.1016/j.tig.2007.12.006
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
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors, Bioinformatics, vol.16, issue.8, pp.699-706, 2000. ,
DOI : 10.1093/bioinformatics/16.8.699
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
Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms, Genomics, vol.11, issue.3, pp.635-650, 1991. ,
DOI : 10.1016/0888-7543(91)90071-L
Bio-sequence database scanning on a GPU, Proceedings of the 20th IEEE International Parallel & Distributed Processing Symposium, 2006. ,
Exploring the viability of the Cell Broadband Engine for bioinformatics applications, Proceedings of IEEE International Parallel and Distributed Processing Symposium, pp.1-8, 2007. ,
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
DOI : 10.1016/S0022-2836(05)80360-2
FPGA-accelerated seed generation in Mercury BLASTP, 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2007), pp.95-106, 2007. ,
DOI : 10.1109/FCCM.2007.11
A reconfigurable index FLASH memory tailored to seed-based genomic sequence somparison algorithms. VLSI Signal Processing, pp.255-269, 2007. ,
FPGA-based accelerators for BLAST families with multi-seeds detection and parallel extension, Proceedings of the 2nd International Conference, pp.58-62, 2008. ,
Accelerating BLASTP on the Cell Broadband Engine, Proceedings of Pattern Recognition in Bioinformatics, Third IAPR International Conference, pp.460-470, 2008. ,
DOI : 10.1007/978-3-540-88436-1_39
On Subset Seeds for Protein Alignment, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.6, issue.3, pp.483-494, 2009. ,
DOI : 10.1109/TCBB.2009.4
URL : https://hal.archives-ouvertes.fr/inria-00354773
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.253389-3402, 1997. ,
DOI : 10.1093/nar/25.17.3389
Aligning two sequences within a specified diagonal band, Bioinformatics, vol.8, issue.5, pp.481-487, 1992. ,
DOI : 10.1093/bioinformatics/8.5.481
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/8/5/481
[27] Local alignment statistics, Methods Enzymol, vol.266, pp.460-480, 1996. ,
DOI : 10.1016/S0076-6879(96)66029-7
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes., Proceedings of the National Academy of Sciences, vol.87, issue.6, pp.2264-2268, 1990. ,
DOI : 10.1073/pnas.87.6.2264
The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions, Bioinformatics, vol.21, issue.7, pp.902-911, 2005. ,
DOI : 10.1093/bioinformatics/bti070
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
DOI : 10.1016/S0022-2836(05)80360-2
Assessing sequence comparison methods with the average precision criterion, Bioinformatics, vol.19, issue.18, pp.2456-2460, 2003. ,
DOI : 10.1093/bioinformatics/btg349
Fpga-based accelerators for blast families with multi-seeds detection and parallel extension, The 2nd International Conference, pp.58-62, 2008. ,
Composition-based statistics and translated nucleotide searches: Improving the tblastn module of blast, BMC Biology, 2006. ,
Amino acid substitution matrices from protein blocks., Proc. Natl. Acad. Sci. USA, pp.10915-10919, 1992. ,
DOI : 10.1073/pnas.89.22.10915
A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms, The Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology, vol.85, issue.11, pp.255-269, 2007. ,
DOI : 10.1007/s11265-007-0073-6
URL : https://hal.archives-ouvertes.fr/inria-00178314
The impact of next-generation sequencing technology on genetics, Trends in Genetics, vol.24, issue.3, pp.133-141, 2008. ,
DOI : 10.1016/j.tig.2007.12.007
Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware, Parallel Bio-Computing (PBC-07) ,
DOI : 10.1007/978-3-540-68111-3_131
URL : https://hal.archives-ouvertes.fr/inria-00178325
Bioinformatics challenges of new sequencing technology [1] The Universal Protein Resource (UniProt) The UniProt Consortium Next-generation DNA sequencing Improved tools for biological sequence comparison, Reconfigurable Computing: Accelerating Computation with Field-Programmable Gate Arrays Proc. National Academy of Science, pp.142-149, 1988. ,
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
DOI : 10.1016/S0022-2836(05)80360-2
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997. ,
DOI : 10.1093/nar/25.17.3389
RC-BLAST: Towards a Portable, Cost-Effective Open Source Hardware Implementation, 19th IEEE International Parallel and Distributed Processing Symposium, 2005. ,
DOI : 10.1109/IPDPS.2005.373
accelerating protein sequence alignment A recofigurable index flash memory tailored to seed-based genomic sequence comparison algorithms, ACM Transactions on Reconfigurable Technology and System VLSI Signal Processing, vol.111, issue.483, pp.255-269, 2007. ,
High performance FPGA-based core for BLAST sequence alignment with the two-hit method Single pass, BLAST-Like, approximate string matching on FPGAs Protein similarity search with subset seeds on a dedicated reconfigurable hardware: Parallel Local Alignment search Tool for Database comparison Fine-grained parallelization of similarity search between protein sequences, Reconfigurable Computing: Architectures, Tools and Applications 8th IEEE International Conference on BioInformatics and BioEngineering Field-Programmable Custom Computing Machines Parallel Bio-Computing, pp.39-50, 2006. ,
version multi-c÷ur SSE) sur un cluster de machines en utilisant la librairie MPI. Cette implémentation utilise l'approche de mpiBLAST [15] qui partitionne et répartit une banque de séquences sur les n÷uds d'un cluster. La première section introduit le contexte de l'implémentation de BLAST sur des architectures à mémoire partagée et distribuée. L'algorithme de mpiBLAST est décrit dans la section suivante. La troisième section présente l'implémentation de mpiPLAST et évalue ses performances Conclusion et perspectives ,
4 Analyse de sensibilité de BLASTP et PLASTP pour le quatrième jeu de données, p.106 ,
Le logiciel PLAST recherche d'alignements locaux entre deux banques de séquences génomiques (séquences protéiques et séquences d'ADN) Le logiciel PLAST se décline en plusieurs versions suivant les cibles technologiques visées : multi-coeur SSE, cartes graphiques ,
GNU) Changer dans le répertoire contenant PLAST Compiler : make Windows (MinGW -Minimalist GNU for Windows) Changer dans le répertoire contenant PLAST Compiler : mingw-make ,
lib CUDA_COMMONDIR=/path/to/cuda/common Compiler : make 3. RCC-PLAST Installer SGI-RASC Charger le bitstrem de PLAST Changer dans le répertoire contenant RCC-PLAST Modier Makele RASC_INCLUDE=/path/to/rasc/include Complier : make 4. mpiPLAST Installer MPICH ou LAM/MPI Changer dans le répertoire contenant mpiPLAST Complier : make Exécution $ plastall -p <prog> -d </path ,
Basic local alignment search tool, J Mol Biol, vol.215, issue.3, p.403410, 1990. ,
Gapped BLAST and PSI- BLAST : a new generation of protein database search programs, Nucleic Acids Research, issue.17, p.2533893402, 1997. ,
PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, p.440445, 2002. ,
DOI : 10.1093/bioinformatics/18.3.440
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.147.8001
PATTERNHUNTER II: HIGHLY SENSITIVE AND FAST HOMOLOGY SEARCH, Journal of Bioinformatics and Computational Biology, vol.02, issue.03, p.417439, 2004. ,
DOI : 10.1142/S0219720004000661
Ecient seeding techniques for protein similarity search, Bioinformatics Research and Development, Second International Conference, p.466478, 2008. ,
On Subset Seeds for Protein Alignment, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.6, issue.3 ,
DOI : 10.1109/TCBB.2009.4
URL : https://hal.archives-ouvertes.fr/inria-00354773
BLAT---The BLAST-Like Alignment Tool, Genome Research, vol.12, issue.4, pp.656-664, 2002. ,
DOI : 10.1101/gr.229202
A recongurable index ash memory tailored to seed-based genomic sequence comparison algorithms, VLSI Signal Processing, vol.48, issue.3, p.255269, 2007. ,
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors, Bioinformatics, vol.16, issue.8, p.699706, 2000. ,
DOI : 10.1093/bioinformatics/16.8.699
Striped Smith-Waterman speeds database searches six times over other SIMD implementations, Bioinformatics, vol.23, issue.2, p.156161, 2007. ,
DOI : 10.1093/bioinformatics/btl582
CUDA compatible GPU cards as ecient hardware accelerators for smith-waterman sequence alignment, BMC Bioinformatics, issue.9 2, 2008. ,
Mercury BLASTP : accelerating protein sequence alignment, ACM Transactions on Recongurable Technology and System, vol.1, issue.2, 2008. ,
Improved gapped alignment in BLAST, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.1, issue.3, pp.116-129, 2004. ,
DOI : 10.1109/TCBB.2004.32
The design, implementation, and evaluation of mpiblast, Proceedings of Conference on Linux Cluster : The HPC Revolution, 2003. ,
Basic principles of ROC analysis, Seminars in nuclear medicine, p.283298, 1978. ,
DOI : 10.1016/S0001-2998(78)80014-2
DDBJ working on evaluation and classication of bacterial genes in INSDC, Nucleic Acids Research, vol.35, p.1315, 2007. ,
EMBL nucleotide seequence database in 2006, Nucleic Acids Research, vol.35, p.1620, 2007. ,
Cramming more components onto integrated circuits, Electronics, vol.38, issue.8, 1965. ,
Amino acid substitution matrices from protein blocks, Proc. Natl. Acad. Sci. USA, p.1091510919, 1992. ,
Amino acid substitution matrices from an information theoretic perspective, J Mol Biol, vol.219, issue.3, p.555565, 1991. ,
Methods for assessing the statistical signicance of molecular sequence features by using general scoring schemes, Proc Natl Acad Sci U S A, vol.87, issue.6, p.22642268, 1990. ,
Local alignment statistics, Methods Enzymol, vol.266, pp.460-480, 1996. ,
A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, vol.48, issue.3, p.443453, 1970. ,
Identication of common molecular subsequences, Journal of Molecular Biology, vol.147, issue.1, p.195197, 1981. ,
Rapid and sensitive protein similarity searches, Science, vol.227, issue.4693, p.14351441, 1985. ,
Improved tools for biological sequence comparison, Proc Natl Acad Sci U S A, vol.85, issue.8, p.24442448, 1988. ,
Finding motifs using random projections, Proceedings of the Fifth Annual International Conference on Computational Biology, p.6976, 2001. ,
DOI : 10.1089/10665270252935430
URL : http://b.web.umkc.edu/bic/projection02.pdf
Provably sensitive indexing strategies for biosequence similarity search, RECOMB, p.9099, 2002. ,
Better ltering with gapped q-grams, Proceedings of the 12th Symposium on Combinatorial Pattern Matching (CPM), p.7385, 2001. ,
DOI : 10.1007/3-540-48194-x_6
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.13.5942
Improved hit criteria for DNA local alignment, BMC Bioinformatics, 2004. ,
YASS: enhancing the sensitivity of DNA similarity search, Nucleic Acids Research, vol.33, issue.Web Server, p.540543, 2005. ,
DOI : 10.1093/nar/gki478
Designing multiple simultaneous seeds for DNA similarity search, Proceedings of the 8th Annual International Conference on Computational Molecular Biology (RECOMB), pp.76-84, 2004. ,
DOI : 10.1145/974614.974625
URL : http://ai.stanford.edu/~serafim/CS374_2006/papers/SunBuhler_Indexing.pdf
Optimizing multiple spaced seeds for homology search, Proceedings of the 15th Symposium on Combinatorial Pattern Matching (CPM), p.4758, 2004. ,
DOI : 10.1007/978-3-540-27801-6_4
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.139.2079
Ecient methods for generating optimal single and multiple spaced seeds, Proceedings of the IEEE 4th Symposium on Bioinformatics and Bioengineering (BIBE), p.411416, 2004. ,
Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specificity, WABI, p.3954, 2003. ,
DOI : 10.1007/978-3-540-39763-2_4
Multiple vector seeds for protein alignment, Proceedings of the 4th International Workshop in Algorithms in Bioinformatics (WABI), p.170181, 2004. ,
Vector seeds: An extension to spaced seeds, Journal of Computer and System Sciences, vol.70, issue.3, p.364380, 2005. ,
DOI : 10.1016/j.jcss.2004.12.008
Optimizing multiple seed for protein homology search ,
A UNIFYING FRAMEWORK FOR SEED SENSITIVITY AND ITS APPLICATION TO SUBSET SEEDS, Journal of Bioinformatics and Computational Biology, vol.04, issue.02, p.553569, 2006. ,
DOI : 10.1142/S0219720006001977
URL : https://hal.archives-ouvertes.fr/inria-00001164
Protein similarity search with subset seeds on a dedicated recongurable hardware, Parallel Bio-Computing, 2007. ,
Ecient algorithms for folding and comparing nucleic acid sequences, p.197206, 1982. ,
DOI : 10.1093/nar/10.1.197
URL : http://doi.org/10.1093/nar/10.1.197
A rapid access motif database (RAMdb) with a search algorithm for the retrieval patterns in nucleic acids or protein databanks, Bioinformatics, vol.11, issue.3, p.273279, 1995. ,
DOI : 10.1093/bioinformatics/11.3.273
FLASH: a fast look-up algorithm for string homology, Proceedings of IEEE Conference on Computer Vision and Pattern Recognition, p.5664, 1993. ,
DOI : 10.1109/CVPR.1993.341106
SSAHA: A Fast Search Method for Large DNA Databases, Genome Research, vol.11, issue.10, p.17251729, 2001. ,
DOI : 10.1101/gr.194201
Composition-based statistics and translated nucleotide searches : Improving the TBLASTN module of BLAST, BMC Biology, 2006. ,
miBLAST : scalable evaluation of a batch of nucleotide sequence queries with BLAST, Nucleic Acids Research, vol.33, issue.13, p.433544, 2005. ,
Linear pattern matching algorithms, 14th Annual Symposium on Switching and Automata Theory (swat 1973), p.111, 1973. ,
DOI : 10.1109/SWAT.1973.13
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.474.9582
Reducing the space requirement of sux trees, Softw. Pract. Exper, vol.29, issue.13, p.11491171, 1999. ,
REPuter: fast computation of maximal repeats in complete genomes, Bioinformatics, vol.15, issue.5, p.426427, 1999. ,
DOI : 10.1093/bioinformatics/15.5.426
REPuter: the manifold applications of repeat analysis on a genomic scale, Nucleic Acids Research, vol.29, issue.22, p.2946334642, 2001. ,
DOI : 10.1093/nar/29.22.4633
Alignment of whole genomes, Nucleic Acids Res, vol.30, issue.11, p.236976, 1999. ,
Fast algorithms for large-scale genome alignment and comparison, Nucleic Acids Res, vol.27, issue.11, p.247883, 2002. ,
Replacing sux trees with enhanced sux arrays, Journal of Discrete Algorithms, vol.2, issue.1, p.5386, 2004. ,
Compressed indexing for genomic retrieval, Journal of Mathematical . Modelling and Scientic Computing, vol.9, issue.2, p.144154, 1998. ,
Cafe, Proceedings of the 21st annual international ACM SIGIR conference on Research and development in information retrieval , SIGIR '98, p.389, 1998. ,
DOI : 10.1145/290941.291078
Indexing and retrieval for genomic databases ,
Self-indexing inverted les for fast text retrieval ,
Finding approximate matches in large lexicons, Software: Practice and Experience, vol.15, issue.3, p.331345, 1995. ,
DOI : 10.1002/spe.4380250307
Microparallelism and highperformance protein matching, Proceeding of the Supercomputing Conference, p.38, 1995. ,
Using video-oriented instructions to speed up sequence comparison, Bioinformatics, vol.13, issue.2, p.145150, 1997. ,
DOI : 10.1093/bioinformatics/13.2.145
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/13/2/145
Searching protein sequence libraries : Comparison of the sensitivity and selectivity of the smith-waterman and fasta algorithms, Genomics, vol.11, p.635650, 1991. ,
ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches, Nucleic Acids Research, vol.29, issue.7, p.16471652, 2001. ,
DOI : 10.1093/nar/29.7.1647
ParAlign : rapid and sensitive sequence similarity searches powered by parallel computing technology, Nucleic Acids Res, vol.33, p.5359, 2005. ,
GPU Accelerated Smith-Waterman, International Conference on Computational Science, p.188195, 2006. ,
DOI : 10.1007/11758549_29
Introduction to the Cell multiprocessor, IBM Journal of Research and Development, vol.49, issue.4.5, 2005. ,
DOI : 10.1147/rd.494.0589
Cell Multiprocessor Communication Network: Built for Speed, IEEE Micro, vol.26, issue.3, p.1023, 2006. ,
DOI : 10.1109/MM.2006.49
Exploring the viability of the cell broadband engine for bioinformatics applications ,
Optimizing smith-waterman for the cell broadband engine, 200818. ,
Accelerating BLASTP on the Cell Broadband Engine, In Pattern Recognition in Bioinformatics, p.460470, 2008. ,
DOI : 10.1007/978-3-540-88436-1_39
A deterministic nite automaton for faster protein hit detection in BLAST, Journal of Computational Biology, vol.13, issue.4, p.965978, 2006. ,
Three Complementary Approaches to Parallelization of Local BLAST Service on Workstation Clusters, PaCT '999 : Proceedings of the 5th International Conference on Parallel Computing Technologies, p.271282, 1999. ,
DOI : 10.1007/3-540-48387-X_29
Recongurable computing in real-world applications. FPGA and Programmable Logic, 2006. ,
Hardware Accelerator for Genomic Sequence Alignment, 2006 International Conference of the IEEE Engineering in Medicine and Biology Society, p.57875789, 2006. ,
DOI : 10.1109/IEMBS.2006.260286
160-fold acceleration of the smithwaterman algorithm using a eld programmable gate array (fpga), BMC Bioinformatics, vol.8, 2007. ,
High speed homology search using run-time reconguration, 12th International Conference on Field-Programmable Logic and Applications, Recongurable Computing Is Going Mainstream, p.281291, 2002. ,
DOI : 10.1007/3-540-46117-5_30
Algorithms for VLSI processors arrays, 1980. ,
A systolic array for rapid string comparison, Chapel Hill Conf. on VLSI, H. Fuchs, p.363376, 1985. ,
Biological information signal processor, Proceedings of the International Conference on Application Specific Array Processors, p.144160, 1991. ,
DOI : 10.1109/ASAP.1991.238887
Searching genetic databases on Splash 2, Proceedings. IEEE Workshop on FPGAs for Custom Computing Machines, p.185191, 1993. ,
A systolic array architecture for the Smith-Waterman algorithm with high performance cell design, Proceedings of IADIS European Conference on Data Mining, p.3542, 2008. ,
Mercury BLASTN : faster DNA sequence comparison using a streaming hardware architecture, Recongurable Systems Summer Institute, 2007. ,
Mitron-accelerated BLAST, 2007. ,
RC-BLAST: Towards a Portable, Cost-Effective Open Source Hardware Implementation, 19th IEEE International Parallel and Distributed Processing Symposium, 2005. ,
DOI : 10.1109/IPDPS.2005.373
BLAST implementation on BEE2. Electrical Engineering and Computer ScienceUniversity of California at Berkeley ,
A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP, 2007 International Conference on Field Programmable Logic and Applications, p.765769, 2007. ,
DOI : 10.1109/FPL.2007.4380764
Hardware BLAST Algorithms with Multi-seeds Detection and Parallel Extension, Recongurable Computing : Architectures, Tools and Applications, 4th International Workshop, p.3950, 2008. ,
DOI : 10.1007/978-3-540-78610-8_7
High performance FPGA-based core for BLAST sequence alignment with the two-hit method, 2008 8th IEEE International Conference on BioInformatics and BioEngineering, p.17, 2008. ,
DOI : 10.1109/BIBE.2008.4696722
Design and implementation of an FPGA-based core for gapped BLAST sequence alignment with the two-hit method. International Association Of Engineers, 2008. ,
Single pass, BLAST-Like, approximate string matching on FPGAs, 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, p.217226, 2006. ,
Ecient data access for parallel BLAST, Proceedings of 19th IEEE International on Parallel and Distributed Processing Symposium, 2005. ,
Parallel genomic sequence-search on a massively parallel system, Proceedings of the 4th international conference on Computing frontiers , CF '07, p.5968, 2007. ,
DOI : 10.1145/1242531.1242542
OpenCL specication v1.0, 2008. ,
Mitrion- C application development on SGI Altix 350/RC100, IEEE Symposium on Field-Programmable Custom Computing Machines, p.239250, 2007. ,
An FPGA power aware design ow, Power and Timing Modeling, Optimization and Simulation, 16th International Workshop, p.415424, 2006. ,
ClustalW-MPI : ClustalW analysis using distributed and parallel computing, Bioinformatics, vol.19, issue.12, p.15851586, 2003. ,
HMPP : A hybrid multicore parallel programming environment. http://www.caps-entreprise.com/ caps-hmpp-gpgpu-Boston-Workshop, 2007. ,
Exemples de l'extension sans gap de BLAST ,