Speeding up the dialign multiple alignment program by using the 'greedy alignment of biological sequences library' (gabios-lib), In JOBIM, pp.1-11, 2000. ,
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
Ttargeting death and decoy receptors of the tumour-necrosis factor superfamily, Nature Reviews Cancer, 2002. ,
Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Second International Conference on Intelligent Systems for Molecular Biology, 1994. ,
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner, Genome Research, vol.14, issue.4, pp.708-715, 2004. ,
DOI : 10.1101/gr.1933104
Approaches to the Automatic Discovery of Patterns in Biosequences, Journal of Computational Biology, vol.5, issue.2, pp.277-304, 1998. ,
DOI : 10.1089/cmb.1998.5.279
SPLASH: structural pattern localization analysis by sequential histograms, Bioinformatics, vol.16, issue.4, pp.341-357, 2000. ,
DOI : 10.1093/bioinformatics/16.4.341
What is the search space for the inference of nondeterministic, unambiguous and deterministic automata ?, 2003. ,
A Similar Fragments Merging Approach to Learn Automata on Proteins, ECML, pp.522-529, 2005. ,
DOI : 10.1007/11564096_50
URL : https://hal.archives-ouvertes.fr/inria-00070340
Apprentissage d'automates par fusions de paires de fragments significativement similaires etpremì eres expérimentations sur les protéines mip, In JOBIM, 2004. ,
Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids, 1999. ,
DOI : 10.1017/CBO9780511790492
MIPDB: a relational database dedicated to MIP family proteins, Biology of the Cell, vol.99, issue.7, pp.535-543, 2005. ,
DOI : 10.1042/BC20040123
URL : https://hal.archives-ouvertes.fr/hal-00107987
Amino acid substitution matrices from protein blocks., Proc. Natl. Acad. Sci. USA, pp.10915-10919, 1992. ,
DOI : 10.1073/pnas.89.22.10915
MoDEL: an efficient strategy for ungapped local multiple alignment, Computational Biology and Chemistry, vol.28, issue.2, pp.119-128, 2004. ,
DOI : 10.1016/j.compbiolchem.2004.01.001
A generic motif discovery algorithm for sequential data, Bioinformatics, vol.22, issue.1, 2005. ,
DOI : 10.1093/bioinformatics/bti745
Finding flexible patterns in unaligned protein sequences, Protein Science, vol.22, issue.8, pp.1587-1595, 1995. ,
DOI : 10.1002/pro.5560040817
Hidden Markov models for detecting remote protein homologies, Bioinformatics, vol.14, issue.10, pp.846-865, 1998. ,
DOI : 10.1093/bioinformatics/14.10.846
Results of the Abbadingo one DFA learning competition and a new evidence-driven state merging algorithm, Lecture Notes in Computer Science, vol.1433, pp.1-12, 1998. ,
DOI : 10.1007/BFb0054059
Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment, Science, vol.262, issue.5131 ,
DOI : 10.1126/science.8211139
Multiple sequence alignment using partial order graphs, Bioinformatics, vol.18, issue.3, pp.452-464, 2002. ,
DOI : 10.1093/bioinformatics/18.3.452
Indice probabiliste discriminant de vraisemblance du lien pour des données volumineuses. RNTI-E-1, numéro spécial, pp.69-94, 2004. ,
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment, Bioinformatics, vol.15, issue.3, pp.211-218, 1999. ,
DOI : 10.1093/bioinformatics/15.3.211
Identifying hierarchical structure in sequences: A linear-time algorithm, Journal of Artificial Intelligence Research, vol.7, pp.67-82, 1997. ,
Highly specific protein sequence motifs for genome analysis, Proceedings of the National Academy of Sciences, vol.95, issue.11, pp.955865-5871, 1998. ,
DOI : 10.1073/pnas.95.11.5865
Inferring regular languages in polynomial update time, Pattern Recognition and Image Analysis, pp.49-61, 1992. ,
De Novo Repeat Classification and Fragment Assembly, Genome Research, vol.14, issue.9, pp.1786-1796, 2004. ,
DOI : 10.1101/gr.2395204
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm [published erratum appears in Bioinformatics 1998;14(2):229], Bioinformatics, vol.14, issue.1, pp.55-67, 1998. ,
DOI : 10.1093/bioinformatics/14.1.55
The Emergence of Pattern Discovery Techniques in Computational Biology, Metabolic Engineering, vol.2, issue.3, pp.159-177, 2000. ,
DOI : 10.1006/mben.2000.0151
Hmmer user's guide: biological sequence analysis using prole hidden markov models, 1998. ,
Grammatical inference in bioinformatics, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol.27, issue.7, pp.1051-1062, 2005. ,
DOI : 10.1109/TPAMI.2005.140
The language of genes, Nature, vol.10, issue.6912, pp.211-217, 2002. ,
DOI : 10.1038/29667
Unsupervised learning of natural languages, Proceedings of the National Academy of Sciences, vol.102, issue.33, pp.11629-11634, 2005. ,
DOI : 10.1073/pnas.0409746102
The classification of amino acid conservation, Journal of Theoretical Biology, vol.119, issue.2, pp.205-218, 1986. ,
DOI : 10.1016/S0022-5193(86)80075-3
Learning non-deterministic finite automata from queries and counterexamples, Machine Intelligence, vol.13, pp.169-189, 1994. ,
InterProScan - an integration platform for the signature-recognition methods in InterPro, Bioinformatics, vol.17, issue.9, pp.847-848, 2001. ,
DOI : 10.1093/bioinformatics/17.9.847