A bit-string longest-common-subsequence algorithm, Information Processing Letters, vol.23, issue.5, pp.305-310, 1986. ,
DOI : 10.1016/0020-0190(86)90091-8
Basic local alignment search tool, Journal of molecular biology, vol.215, issue.3, pp.403-410, 1990. ,
Maximum Contact Map Overlap Revisited, Journal of Computational Biology, vol.18, issue.1, pp.27-41, 2011. ,
DOI : 10.1089/cmb.2009.0196
URL : https://hal.archives-ouvertes.fr/inria-00536624
Solving path problems on the GPU, Parallel Computing, vol.36, issue.5-6, pp.241-253, 2010. ,
DOI : 10.1016/j.parco.2009.12.002
Empirical threshold values for quantitative trait mapping, Genetics, vol.138, issue.3, p.963, 1994. ,
Graphics Processing Unit???Accelerated Quantitative Trait Loci Detection, Journal of Computational Biology, vol.20, issue.9, pp.672-686, 2013. ,
DOI : 10.1089/cmb.2012.0136
URL : https://hal.archives-ouvertes.fr/hal-00903794
A fast and practical bit-vector algorithm for the Longest Common Subsequence problem, Information Processing Letters, vol.80, issue.6, pp.279-285, 2001. ,
DOI : 10.1016/S0020-0190(01)00182-X
Introduction to Algorithms, 2001. ,
Bit-parallel algorithm for the constrained longest common subsequence problem, Fundamenta Informaticae, vol.99, issue.4, pp.409-433, 2010. ,
A note on two problems in connexion with graphs. Numerische mathematik, pp.269-271, 1959. ,
OpenMP: an industry standard API for shared-memory programming, IEEE Computational Science and Engineering, vol.5, issue.1, pp.46-55, 1998. ,
DOI : 10.1109/99.660313
Muscle, BMC bioinformatics, vol.5, issue.1, p.113, 2004. ,
DOI : 10.1007/978-1-349-13443-4_4
URL : https://hal.archives-ouvertes.fr/hal-00897814
Alternative models for QTL detection in livestock . i. general introduction, Genet. Sel. Evol, vol.31, issue.10, pp.1-121297, 1186. ,
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
Extensive genome-wide linkage disequilibrium in cattle, Genome Res, vol.10, pp.220-227, 2000. ,
Optimal haplotype reconstruction in half-sib families, ICLP-10 workshop on Constraint Based Methods for Bioinformatics, 2010. ,
QTLMap, a software for QTL detection in outbred populations, Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, pp.1-6, 2010. ,
Fast Algorithms for Shortest Paths in Planar Graphs, with Applications, SIAM Journal on Computing, vol.16, issue.6, pp.1004-1022, 1987. ,
DOI : 10.1137/0216064
A Comprehensive Performance Comparison of CUDA and OpenCL, 2011 International Conference on Parallel Processing, pp.216-225, 2011. ,
DOI : 10.1109/ICPP.2011.45
Alternative models for QTL detection in livestock. III. Heteroskedastic model and models corresponding to several distributions of the QTL effect, Genetics Selection Evolution, vol.31, issue.4, pp.341-350, 1999. ,
DOI : 10.1186/1297-9686-31-4-341
URL : https://hal.archives-ouvertes.fr/hal-00199719
QTLMap, a software for QTL detection in outbred populations, In Annals of Human Genetics, vol.72, pp.694-694, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-01193540
Using MPI-: Portable Parallel Programming with the Message Passing Interface, 1999. ,
Surprising similarities in structure comparison, Current Opinion in Structural Biology, vol.6, issue.3, pp.377-385, 1996. ,
DOI : 10.1016/S0959-440X(96)80058-3
Evaluating graph coloring on GPUs, ACM SIGPLAN Notices, vol.46, issue.8, p.297, 2011. ,
DOI : 10.1145/2038037.1941597
Big data: The future of biocuration, Nature, vol.2, issue.7209, pp.45547-50, 2008. ,
DOI : 10.1038/455047a
Accelerating Large Graph Algorithms on the GPU Using CUDA, High performance computing?HiPC, pp.197-208, 2007. ,
DOI : 10.1007/978-3-540-77220-0_21
CULA: hybrid GPU accelerated linear algebra routines, Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, p.1, 2010. ,
Linkage disequilibrium in finite populations, Theoretical and Applied Genetics, vol.19, issue.6, pp.226-231, 1968. ,
DOI : 10.1007/BF01245622
EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards, Bioinformatics, vol.27, issue.11, pp.1462-1465, 2011. ,
DOI : 10.1093/bioinformatics/btr172
Bit-parallel LCS-length computation revisited, Proc. 15th Australasian Workshop on Combinatorial Algorithms, pp.16-27, 2004. ,
Hypothesizing about Causal Networks with Positive and Negative Effects by Meta-level Abduction, Inductive Logic Programming, pp.114-129, 2011. ,
DOI : 10.1007/978-3-642-21295-6_15
Reducibility among combinatorial problems ,
An improved algorithm to find the length of the longest common subsequence of two strings, ACM SIGIR Forum, pp.89-99, 1989. ,
DOI : 10.1145/74697.74702
A performance comparison of CUDA and OpenCL. arXiv preprint, 2010. ,
Methods for multiple-marker mapping of quantitative trait loci in half-sib populations, Theoretical and Applied Genetics, vol.93, issue.1-2, pp.71-80, 1007. ,
DOI : 10.1007/BF00225729
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment, Bioinformatics, vol.26, issue.9, pp.1160-1168, 2010. ,
DOI : 10.1093/bioinformatics/btq100
A Fast and High Quality Multilevel Scheme for Partitioning Irregular Graphs, SIAM Journal on Scientific Computing, vol.20, issue.1, pp.359-392, 1998. ,
DOI : 10.1137/S1064827595287997
Parallel multilevel k-way partitioning scheme for irregular graphs, Proceedings of the 1996 ACM/IEEE conference on Supercomputing (CDROM) , Supercomputing '96, pp.96-129, 1998. ,
DOI : 10.1145/369028.369103
All-pairs shortest-paths for large graphs on the GPU, Proceedings of the 23rd ACM SIG- GRAPH/EUROGRAPHICS symposium on Graphics hardware, GH '08, pp.47-55, 2008. ,
Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures, Journal of Molecular Biology, vol.346, issue.4, pp.1173-1188, 2005. ,
DOI : 10.1016/j.jmb.2004.12.032
A BIT-PARALLEL DYNAMIC PROGRAMMING ALGORITHM SUITABLE FOR DNA SEQUENCE ALIGNMENT, Journal of Bioinformatics and Computational Biology, vol.10, issue.04, pp.10-2012 ,
DOI : 10.1142/S0219720012500023
Parallelization of the MAFFT multiple sequence alignment program, Bioinformatics, vol.26, issue.15, pp.1899-1900, 2010. ,
DOI : 10.1093/bioinformatics/btq224
PLAST: parallel local alignment search tool for database comparison, BMC bioinformatics, vol.10, issue.1, p.329, 2009. ,
URL : https://hal.archives-ouvertes.fr/inria-00425301
Fast determination of the optimal rotational matrix for macromolecular superpositions, Journal of Computational Chemistry, vol.450, issue.Suppl 2, pp.311561-1563, 2010. ,
DOI : 10.1002/jcc.21439
The interaction of selection and linkage. II. Optimum models, Genetics, vol.50, pp.757-782, 1964. ,
Linear models for joint association and linkage QTL mapping, Genetics Selection Evolution, vol.41, issue.1, p.43, 2009. ,
DOI : 10.1186/1297-9686-41-43
GPU Accelerated Smith-Waterman, Computational Science?ICCS 2006, pp.188-195, 2006. ,
DOI : 10.1007/11758549_29
Predicting positive and negative links in online social networks, Proceedings of the 19th international conference on World wide web, WWW '10, pp.641-650, 2010. ,
DOI : 10.1145/1772690.1772756
Community Structure in Large Networks: Natural Cluster Sizes and the Absence of Large Well-Defined Clusters, Internet Mathematics, vol.6, issue.1, pp.29-123, 2009. ,
DOI : 10.1080/15427951.2009.10129177
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, pp.1-8, 2009. ,
DOI : 10.1109/IPDPS.2009.5160931
An algorithm for QTL detection in mixture of full and half-sib families, Proceedings of the 6th World Congress on Genetics Applied to Livestock Production, pp.257-260, 1998. ,
Anomalies in parallel branch-and-bound algorithms, Communications of the ACM, vol.27, issue.6, pp.594-602, 1984. ,
DOI : 10.1145/358080.358103
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. ,
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
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities, Bioinformatics, vol.26, issue.16, pp.261958-1964, 2010. ,
DOI : 10.1093/bioinformatics/btq338
GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment, High Performance Computing-HiPC, pp.363-374, 2006. ,
DOI : 10.1007/11945918_37
Big data: How do your data grow?, Nature, vol.455, issue.7209, pp.28-29, 2008. ,
DOI : 10.1038/455028a
Cramming more components onto integrated circuits, 1965. ,
An Experimental Study of a Parallel Shortest Path Algorithm for Solving Large-Scale Graph Instances, ALENEX. SIAM, 2007. ,
DOI : 10.1137/1.9781611972870.3
Maximum Cliques in Protein Structure Comparison, Experimental Algorithms, pp.106-117, 2010. ,
DOI : 10.1007/978-3-642-13193-6_10
URL : https://hal.archives-ouvertes.fr/inria-00536700
Blocked United Algorithm for the All-Pairs Shortest Paths Problem on Hybrid CPU-GPU Systems, IEICE Transactions on Information and Systems, vol.95, issue.12, pp.952759-2768, 2012. ,
DOI : 10.1587/transinf.E95.D.2759
Leda: A platform for combinatorial and geometric computing, 1999. ,
Excerpts from a conversation with gordon moore: Moore's law, 2005. ,
??-stepping: a parallelizable shortest path algorithm, Journal of Algorithms, vol.49, issue.1, pp.114-152, 2003. ,
DOI : 10.1016/S0196-6774(03)00076-2
CUDA compatible GPU cards as efficient hardware accelerators for smith-waterman sequence alignment, BMC bioinformatics, issue.9 2, p.10, 2008. ,
A fast bit-vector algorithm for approximate string matching based on dynamic programming, Journal of the ACM, vol.46, issue.3, pp.395-415, 1999. ,
DOI : 10.1145/316542.316550
A tuned, concurrent-kernel approach to speed up the APSP problem, 2013. ,
A task parallel algorithm for finding all-pairs shortest paths using the GPU, International Journal of High Performance Computing and Networking, vol.7, issue.2, pp.87-98, 2012. ,
DOI : 10.1504/IJHPCN.2012.046384
On-line scheduling of MPI-2 programs with hierarchical work stealing, Computer Architecture and High Performance Computing SBAC-PAD 2007. 19th International Symposium on, pp.247-254, 2007. ,
Threshold and power for Quantitative Trait Locus detection, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00482142
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
Optimal Protein Structure Alignment Using Maximum Cliques, Operations Research, vol.53, issue.3, pp.389-402, 2005. ,
DOI : 10.1287/opre.1040.0189
GridQTL: a grid portal for QTL mapping of compute intensive datasets, Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, pp.13-18, 2006. ,
QTL Express: mapping quantitative trait loci in simple and complex pedigrees, Bioinformatics, vol.18, issue.2, pp.339-340, 2002. ,
DOI : 10.1093/bioinformatics/18.2.339
A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology, Journal of Molecular Biology, vol.323, issue.2, pp.387-406, 2002. ,
DOI : 10.1016/S0022-2836(02)00811-2
Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core, Current Biology, vol.3, issue.3, pp.141-148, 1993. ,
DOI : 10.1016/0960-9822(93)90255-M
DNA sequencing with chain-terminating inhibitors, Proceedings of the National Academy of Sciences, pp.5463-5467, 1977. ,
DOI : 10.1073/pnas.74.12.5463
MPI: the complete reference, 1995. ,
An improved bit parallel exact maximum clique algorithm. Optimization Letters, pp.1-13, 2013. ,
An exact bit-parallel algorithm for the maximum clique problem, Computers & Operations Research, vol.38, issue.2, pp.571-581, 2011. ,
DOI : 10.1016/j.cor.2010.07.019
Finding, Counting and Listing All Triangles in Large Graphs, an Experimental Study, Experimental and Efficient Algorithms, pp.606-609, 2005. ,
DOI : 10.1007/11427186_54
Community detection in networks with positive and negative links, Physical Review E, vol.80, issue.3, p.36115, 2009. ,
DOI : 10.1103/PhysRevE.80.036115
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
A parallel implementation for the maximum clique problem, Journal of Combinatorial Mathematics and Combinatorial Computing, vol.63, p.183, 2007. ,
Constrained multiple sequence alignment tool development and its application to rnase family alignment, Journal of Bioinformatics and Computational Biology, vol.1, issue.02, pp.267-287, 2003. ,
The constrained longest common subsequence problem, Information Processing Letters, vol.88, issue.4, pp.173-176, 2003. ,
DOI : 10.1016/j.ipl.2003.07.001
A Simple and Faster Branch-and-Bound Algorithm for Finding a Maximum Clique, WALCOM: Algorithms and computation, pp.191-203, 2010. ,
DOI : 10.1007/978-3-642-11440-3_18
Parallel multiple alignments and their implementation on CM5, Genome Informatics, vol.4, pp.103-108, 1993. ,
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
Better performance at lower occupancy, Proceedings of the GPU Technology Conference, 2010. ,
GPU-BLAST: using graphics processors to accelerate protein sequence alignment, Bioinformatics, vol.27, issue.2, pp.182-188, 2011. ,
Big data: Wikiomics, Nature, vol.455, issue.7209, p.45522, 2008. ,
DOI : 10.1038/455022a
DALIX: Optimal DALI Protein Structure Alignment, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, issue.1, pp.26-36, 2013. ,
DOI : 10.1109/TCBB.2012.143
A fast multiple longest common subsequence (MLCS) algorithm. Knowledge and Data Engineering, IEEE Transactions on, vol.23, issue.3, pp.321-334, 2011. ,
Using video-oriented instructions to speed up sequence comparison Computer applications in the biosciences, CABIOS, vol.13, issue.2, pp.145-150, 1997. ,
PAUL: protein structural alignment using integer linear programming and Lagrangian relaxation, BMC Bioinformatics, vol.10, issue.Suppl 13, p.2, 2009. ,
DOI : 10.1186/1471-2105-10-S13-P2
Streaming algorithms for biological sequence alignment on GPUs. Parallel and Distributed Systems, IEEE Transactions on, vol.18, issue.9, pp.1270-1281, 2007. ,
Inter-block GPU communication via fast barrier synchronization, Parallel Distributed Processing (IPDPS), 2010 IEEE International Symposium on, pp.1-12, 2010. ,
An efficient parallel algorithm for longest common subsequence problem on GPUs, Proceedings of the world congress on engineering, 2010. ,
Accelerating nucleotide sequence alignment by GPUs ,
Scoring function for automated assessment of protein structure template quality, Proteins: Structure, Function, and Bioinformatics, vol.101, issue.4, pp.702-710, 2004. ,
DOI : 10.1002/prot.20264
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