Parallel position weight matrices algorithms, International Symposium on Parallel and Distributed Computing, pp.65-69, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00623404
JASPAR: an open-access database for eukaryotic transcription factor binding profiles, Nucleic Acids Research, vol.32, issue.90001, pp.91-94, 2004. ,
DOI : 10.1093/nar/gkh012
TRANSFAC: an integrated system for gene expression regulation, Nucleic Acids Research, vol.28, issue.1, pp.316-319, 2000. ,
DOI : 10.1093/nar/28.1.316
Next-generation DNA sequencing, Nature Biotechnology, vol.105, issue.10, pp.1135-1145, 2008. ,
DOI : 10.1038/nbt1486
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing, Nature Methods, vol.128, issue.8, pp.651-657, 2007. ,
DOI : 10.1038/nmeth1068
WebLogo: A Sequence Logo Generator, Genome Research, vol.14, issue.6 ,
DOI : 10.1101/gr.849004
Initial Experiences Porting a Bioinformatics Application to a Graphics Processor, Adv. in Informatics, pp.415-425, 2005. ,
DOI : 10.1007/11573036_39
Müller-Wittig, GPU-ClustalW: using graphics hardware to accelerate multiple sequence alignment, High Performance Computing, pp.363-374, 2006. ,
High-throughput sequence alignment using Graphics Processing Units, BMC Bioinformatics, vol.8, issue.1, p.474, 2007. ,
DOI : 10.1186/1471-2105-8-474
Optimizing data intensive GPGPU computations for DNA sequence alignment, Parallel Computing, vol.35, issue.8-9, pp.429-440, 2009. ,
DOI : 10.1016/j.parco.2009.05.002
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
CUDA???MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units, Pattern Recognition Letters, vol.31, issue.14, 2009. ,
DOI : 10.1016/j.patrec.2009.10.009
Genome-scale Pattern Analysis in the Post-ENCODE Era, 2010. ,
Predicting transcription factor binding sites using local over-representation and comparative genomics, BMC, pp.10-1186 ,
The statistical significance of nucleotide position-weight matrix matches, Bioinformatics, vol.12, issue.5, pp.431-440, 1996. ,
DOI : 10.1093/bioinformatics/12.5.431
Computing exact P-values for DNA motifs, Bioinformatics, vol.23, issue.5, pp.531-537, 2007. ,
DOI : 10.1093/bioinformatics/btl662
Efficient and accurate P-value computation for Position Weight Matrices, Algorithms for Molecular Biology, vol.2, issue.1 ,
DOI : 10.1186/1748-7188-2-15
URL : https://hal.archives-ouvertes.fr/inria-00270263
Similarity of position frequency matrices for transcription factor binding sites, Bioinformatics, vol.21, issue.3, pp.307-313, 2005. ,
DOI : 10.1093/bioinformatics/bth480
Measuring similarities between transcription factor binding sites, BMC Bioinformatics, vol.6, issue.237, pp.1-11, 2005. ,
Quantifying similarity between motifs, Genome Biology, vol.8, issue.2 ,
DOI : 10.1186/gb-2007-8-2-r24
URL : http://doi.org/10.1186/gb-2007-8-2-r24
Natural similarity measures between position frequency matrices with an application to clustering, Bioinformatics, vol.24, issue.3 ,
DOI : 10.1093/bioinformatics/btm610
Fast probabilistic analysis of sequence function using scoring matrices, Bioinformatics, vol.16, issue.3, pp.233-244, 2000. ,
DOI : 10.1093/bioinformatics/16.3.233
Large Scale Matching for Position Weight Matrices, Combinatorial Pattern Matching, pp.401-412, 2006. ,
DOI : 10.1007/11780441_36
URL : https://hal.archives-ouvertes.fr/inria-00270270
Efficient string matching: an aid to bibliographic search, Communications of the ACM, vol.18, issue.6, pp.333-340, 1975. ,
DOI : 10.1145/360825.360855
Fast Pattern Matching in Strings, SIAM Journal on Computing, vol.6, issue.2, pp.323-360, 1977. ,
DOI : 10.1137/0206024
A fast string searching algorithm, Communications of the ACM, vol.20, issue.10, pp.762-772, 1977. ,
DOI : 10.1145/359842.359859
Self-overlapping Occurrences and Knuth-Morris-Pratt Algorithm for Weighted Matching, p.2009 ,
DOI : 10.1007/978-3-540-75530-2_25
URL : https://hal.archives-ouvertes.fr/inria-00365411
Fast Search Algorithms for Position Specific Scoring Matrices, LNCS, vol.4414, pp.239-250, 2007. ,
DOI : 10.1007/978-3-540-71233-6_19
MOODS: fast search for position weight matrix matches in DNA sequences, Bioinformatics, vol.25, issue.23, pp.3181-3182, 2009. ,
DOI : 10.1093/bioinformatics/btp554
Fast index based algorithms and software for matching position specific scoring matrices, BMC Bioinformatics, vol.7 ,
Using sequence compression to speedup probabilistic profile matching, Bioinformatics, vol.21, issue.10, pp.2225-2234, 2005. ,
DOI : 10.1093/bioinformatics/bti323
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/21/10/2225
Bioinformatics Algorithms: Techniques and Applications, 2008, Ch. A survey of seeding for sequence alignment, pp.126-152 ,
DOI : 10.1007/978-3-662-44753-6
Methods for calculating the probabilities of finding patterns in sequences, Bioinformatics, vol.5, issue.2, pp.89-96, 1989. ,
DOI : 10.1093/bioinformatics/5.2.89
Dynamic Programming Algorithms for Two Statistical Problems in Computational Biology, WABI 2003, pp.151-164, 2003. ,
DOI : 10.1007/978-3-540-39763-2_12
The Art of Computer Programming, 1997. ,
The Bioperl Toolkit: Perl Modules for the Life Sciences, Genome Research, vol.12, issue.10, pp.1611-1618, 2002. ,
DOI : 10.1101/gr.361602
BioJava: an open-source framework for bioinformatics, Bioinformatics, vol.24, issue.18, pp.2096-2097, 2008. ,
DOI : 10.1093/bioinformatics/btn397
Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics, Bioinformatics Open Source Conference, 2009. ,