A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction, Evolutionary Bioinformatics, vol.62, issue.7, 2010. ,
DOI : 10.4137/EBO.S4058
Smith-Waterman implementation on a FSB-FPGA module using the Intel Accelerator Abstraction Layer, 2009 IEEE International Symposium on Parallel & Distributed Processing, pp.1-4, 2009. ,
DOI : 10.1109/IPDPS.2009.5161214
Optimal tiling for the RNA base pairing problem, Proceedings of the fourteenth annual ACM symposium on Parallel algorithms and architectures , SPAA '02, p.182, 2002. ,
DOI : 10.1145/564870.564901
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.25-3389, 1997. ,
DOI : 10.1093/nar/25.17.3389
On economical construction of the transitive closure of an oriented graph, In Soviet Math. Dokl, vol.11, p.85, 1970. ,
A genetic algorithm to search for optimal and suboptimal RNA secondary structures, Biophysical Chemistry, vol.55, issue.3, pp.253-259, 1995. ,
DOI : 10.1016/0301-4622(94)00130-C
RNA multistructure landscapes, European Biophysics Journal, vol.22, issue.1, pp.13-24, 1993. ,
A block-sorting lossless data compression algorithm, 1994. ,
PASS: a program to align short sequences, Bioinformatics, vol.25, issue.7, pp.25-967, 2009. ,
DOI : 10.1093/bioinformatics/btp087
Indexing DNA Sequences Using q-Grams, Database Systems for Advanced Applications, pp.4-5, 2005. ,
DOI : 10.1007/11408079_4
Biological information signal processor, Proceedings of the International Conference on Application Specific Array Processors, pp.144-160, 1991. ,
DOI : 10.1109/ASAP.1991.238887
Power Consumption of GPUs from a Software Perspective, Computational Science?ICCS, pp.9-10, 2009. ,
DOI : 10.1007/978-3-642-01970-8_92
URL : https://hal.archives-ouvertes.fr/hal-00348672
Designing efficient FPGA-based accelerator for genomic sequence alignments with ImpulseC high level synthesis tools, 2010. ,
A partition function algorithm for nucleic acid secondary structure including pseudoknots, Journal of Computational Chemistry, vol.350, issue.13, pp.1664-1677, 2003. ,
DOI : 10.1002/jcc.10296
CONTRAfold: RNA secondary structure prediction without physics-based models, Bioinformatics, vol.22, issue.14, pp.22-90, 2006. ,
DOI : 10.1093/bioinformatics/btl246
URL : http://ai.stanford.edu/~serafim/Publications/2006_CONTRAfold.pdf
High similarity sequence comparison in clustering large sequence databases, Proceedings. IEEE Computer Society Bioinformatics Conference, pp.2-2, 2002. ,
DOI : 10.1109/CSB.2002.1039345
Predicting RNA Secondary Structure Using Profile Stochastic Context-Free Grammars and Phylogenic Analysis, Journal of Computer Science and Technology, vol.31, issue.1, pp.582-589, 2008. ,
DOI : 10.1007/s11390-008-9154-7
URL : http://doi.org/10.1007/s11390-008-9154-7
Striped Smith-Waterman speeds database searches six times over other SIMD implementations, Bioinformatics, vol.23, issue.2, p.156, 2007. ,
DOI : 10.1093/bioinformatics/btl582
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/23/2/156
Optimizing smith-waterman for the cell broadband engine, 2008. ,
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers, Journal of Computational Biology, vol.7, issue.1-2, pp.171-182, 2000. ,
DOI : 10.1089/10665270050081441
Opportunistic data structures with applications, Proceedings 41st Annual Symposium on Foundations of Computer Science, p.390, 2000. ,
DOI : 10.1109/SFCS.2000.892127
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.23.7615
A simple, practical and complete O -time Algorithm for RNA folding using the Four-Russians Speedup, Algorithms for Molecular Biology, vol.36, issue.20, p.13, 2010. ,
DOI : 10.1093/nar/gkn544
A comprehensive comparison of comparative RNA structure prediction approaches, BMC Bioinformatics, vol.5, issue.1, p.140, 2004. ,
DOI : 10.1186/1471-2105-5-140
An improved algorithm for matching biological sequences, Journal of Molecular Biology, vol.162, issue.3, pp.705-708, 1982. ,
DOI : 10.1016/0022-2836(82)90398-9
SAMBA: hardware accelerator for biological sequence comparison Direct VLSI implementation of combinatorial algorithms, Proceedings of the Caltech Conference on Very Large Scale Integration: held at the California Institute of Technology, pp.22-24, 1979. ,
RNA folding on parallel computers: The minimum free energy structures of complete HIV genomes, 1995. ,
Schnelle Faltung und Vergleich von Sekund???rstrukturen von RNA, Monatshefte f???r Chemie Chemical Monthly, vol.157, issue.2, pp.1-6, 1994. ,
DOI : 10.1007/BF00818163
BFAST: An Alignment Tool for Large Scale Genome Resequencing, PLoS ONE, vol.5, issue.11, p.7767, 2009. ,
DOI : 10.1371/journal.pone.0007767.s001
Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs, 2008 International Conference on Application-Specific Systems, Architectures and Processors, pp.191-196, 2008. ,
DOI : 10.1109/ASAP.2008.4580177
Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence, 2010 18th IEEE Annual International Symposium on Field-Programmable Custom Computing Machines, 2010. ,
DOI : 10.1109/FCCM.2010.22
MicroRNAs in Drosophila: The magic wand to enter the Chamber of Secrets?, Biochimie, vol.89, issue.10, pp.89-1211, 2007. ,
DOI : 10.1016/j.biochi.2007.05.012
SeqMap: mapping massive amount of oligonucleotides to the genome, Bioinformatics, vol.24, issue.20, pp.24-2395, 2008. ,
DOI : 10.1093/bioinformatics/btn429
Introduction to the Cell multiprocessor, IBM Journal of Research and Development, vol.49, issue.4.5, pp.589-604, 2010. ,
DOI : 10.1147/rd.494.0589
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history, Bioinformatics, vol.15, issue.6, pp.15-446, 1999. ,
DOI : 10.1093/bioinformatics/15.6.446
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.15.9368
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology, vol.10, issue.3, p.25, 2009. ,
DOI : 10.1186/gb-2009-10-3-r25
Ordered index seed algorithm for intensive DNA sequence comparison, 2008 IEEE International Symposium on Parallel and Distributed Processing, 2008. ,
DOI : 10.1109/IPDPS.2008.4536172
URL : https://hal.archives-ouvertes.fr/hal-00322696
Debunking the 100X, 2010. ,
CPU myth: an evaluation of throughput computing on CPU and GPU, Proceedings of the 37th annual international symposium on Computer architecture, pp.451-460 ,
Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum, BMC Genomics, vol.11, issue.1, p.281, 2010. ,
DOI : 10.1186/1471-2164-11-281
URL : https://hal.archives-ouvertes.fr/inserm-00482283
Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, 2009. ,
DOI : 10.1093/bioinformatics/btp324
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234
Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, vol.26, issue.5, p.589, 2010. ,
DOI : 10.1093/bioinformatics/btp698
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828108
Mapping short DNA sequencing reads and calling variants using mapping quality scores, Genome Research, vol.18, issue.11, p.1851, 2008. ,
DOI : 10.1101/gr.078212.108
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577856
160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA), BMC Bioinformatics, vol.8, issue.1, p.185, 2007. ,
DOI : 10.1186/1471-2105-8-185
SOAP: short oligonucleotide alignment program, Bioinformatics, vol.24, issue.5, pp.24-713, 2008. ,
DOI : 10.1093/bioinformatics/btn025
Biosequence database scanning on a GPU, Parallel and Distributed Processing Symposium 20th International, 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
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
P-NAC: A Systolic Array for Comparing Nucleic Acid Sequences, Computer, vol.20, issue.7, pp.9-17, 1987. ,
DOI : 10.1109/MC.1987.1663629
Asymptotics of RNA Shapes, Journal of Computational Biology, vol.15, issue.1, pp.31-63, 2008. ,
DOI : 10.1089/cmb.2006.0153
URL : https://hal.archives-ouvertes.fr/inria-00548861
Internal loops in RNA secondary structure prediction, Proceedings of the third annual international conference on Computational molecular biology , RECOMB '99, pp.260-267, 1999. ,
DOI : 10.1145/299432.299490
PatternHunter: faster and more sensitive homology search CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment, Bioinformatics BMC bioinformatics, vol.18, issue.3 9, p.10, 2002. ,
DINAMelt web server for nucleic acid melting prediction, Nucleic Acids Research, vol.33, issue.Web Server, 2005. ,
DOI : 10.1093/nar/gki591
The equilibrium partition function and base pair binding probabilities for RNA secondary structure, Biopolymers, vol.24, issue.6-7, pp.6-7, 1990. ,
DOI : 10.1002/bip.360290621
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, pp.443-453, 1970. ,
DOI : 10.1016/0022-2836(70)90057-4
SSAHA: A Fast Search Method for Large DNA Databases, Genome Research, vol.11, issue.10, p.1725, 2001. ,
DOI : 10.1101/gr.194201
YASS: enhancing the sensitivity of DNA similarity search, Nucleic Acids Research, vol.33, issue.Web Server, p.540, 2005. ,
DOI : 10.1093/nar/gki478
Algorithms for Loop Matchings, SIAM Journal on Applied Mathematics, vol.35, issue.1, pp.68-82, 1978. ,
DOI : 10.1137/0135006
Reconfigurable architectures for bio-sequence database scanning on FPGAs. Circuits and Systems II: Express Briefs, IEEE Transactions on, issue.12, pp.52-851, 2005. ,
Synthesizing systolic arrays with control signals from recurrence equations. Distributed Computing, pp.8-9, 1989. ,
A dynamic programming algorithm for RNA structure prediction including pseudoknots11Edited by I. Tinoco, Journal of Molecular Biology, vol.285, issue.5, pp.2053-2068, 1999. ,
DOI : 10.1006/jmbi.1998.2436
GPU accelerated RNA folding algorithm, Computational Science?ICCS, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00637827
GASSST: global alignment short sequence search tool, Bioinformatics, vol.26, issue.20, pp.2534-2540, 2010. ,
DOI : 10.1093/bioinformatics/btq485
URL : https://hal.archives-ouvertes.fr/hal-00531499
GPU computing Gems,c hapter GPU accelerated RNA folding algorithm, 2010. ,
DOI : 10.1016/b978-0-12-384988-5.00014-0
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.157.3272
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors, Bioinformatics, vol.16, issue.8, pp.16-699, 2000. ,
DOI : 10.1093/bioinformatics/16.8.699
SHRiMP: Accurate Mapping of Short Color-space Reads, PLoS Computational Biology, vol.8, issue.5, 2009. ,
DOI : 10.1371/journal.pcbi.1000386.t004
Paysage d'énergie et structures localement optimales d'un arn, Journées Ouvertes Biologie Informatique Mathématiques, 2009. ,
CloudBurst: highly sensitive read mapping with MapReduce, Bioinformatics, vol.25, issue.11, pp.25-1363, 2009. ,
DOI : 10.1093/bioinformatics/btp236
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682523
Identification of common molecular subsequences, Journal of Molecular Biology, vol.147, issue.1, pp.5-6, 1981. ,
DOI : 10.1016/0022-2836(81)90087-5
Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data, Journal of biomolecular structure & dynamics, vol.2, issue.3, p.543, 1984. ,
Swps3 fast multi-threaded vectorized smith-waterman for ibm cell/b.e. and x86/sse2, BMC Research Notes, vol.1, issue.107, 2008. ,
Benchmarking GPUs to tune dense linear algebra, 2008 SC, International Conference for High Performance Computing, Networking, Storage and Analysis, pp.1-11, 2008. ,
DOI : 10.1109/SC.2008.5214359
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.218.3436
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
Short read DNA fragment anchoring algorithm, BMC Bioinformatics, vol.10, 2009. ,
CBESW: Sequence Alignment on the Playstation 3, BMC Bioinformatics, vol.9, issue.1, p.377, 2008. ,
DOI : 10.1186/1471-2105-9-377
Using video-oriented instructions to speed up sequence comparison Computer applications in the biosciences, CABIOS, vol.13, issue.2, p.145, 1997. ,
Complete suboptimal folding of RNA and the stability of secondary structures, Biopolymers, vol.4, issue.2, pp.145-165, 1999. ,
DOI : 10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G
Implementation of the Smith-Waterman algorithm on a reconfigurable supercomputing platform, Proceedings of the 1st international workshop on High-performance reconfigurable computing technology and applications held in conjunction with SC07, HPRCTA '07, pp.39-48, 2007. ,
DOI : 10.1145/1328554.1328565
On finding all suboptimal foldings of an RNA molecule, Science, vol.244, issue.4900, pp.244-292, 1989. ,
DOI : 10.1126/science.2468181
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acids Research, vol.9, issue.1, pp.133-148, 1981. ,
DOI : 10.1093/nar/9.1.133