autres méthodes basées sur une analyse comparative, il convient de vérifier certaines propriétés sur les groupes de séquences. Notamment pour les méthodes qui s'appuient sur un alignement, il est nécessaire de s'assurer qu'il est possible de construire un alignement fiable. Dans cette optique, on propose d'´ epurer chaque groupe de séquences enéliminantenéliminant les séquences trop divergentes selon un procédé strictement analoguèanaloguè a celui mis en oeuvre dans Protea et caRNAc pour construire les méta-séquences (section 1.5.3) On proposé ,
Basic local alignment tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison. String Processing and Information Retrieval, pp.348-359, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-00427699
An Overview of Ensembl, Genome Research, vol.14, issue.5, pp.925-928, 2004. ,
DOI : 10.1101/gr.1860604
The Universal Protein Resource (UniProt), Nucleic Acids Research, vol.33, issue.Database issue, pp.154-159, 2005. ,
DOI : 10.1093/nar/gki070
GeneWise and Genomewise, Genome Research, vol.14, issue.5, pp.988-995, 2004. ,
DOI : 10.1101/gr.1865504
Evaluation of Gene Structure Prediction Programs, Genomics, vol.34, issue.3, pp.353-367, 1996. ,
DOI : 10.1006/geno.1996.0298
The PIR-International Protein Sequence Database, Nucleic Acids Research, vol.26, issue.1, pp.27-32, 1998. ,
DOI : 10.1093/nar/26.1.27
An improved algorithm for nucleic acid secondary structure display, Computational Applications in Biosciences, vol.4, issue.1, pp.167-173, 1988. ,
The conserved exon method for gene finding, Proceedings of the 8th International Conference on Intellignet Systems for Molecular Biology ISMB, pp.3-12, 2000. ,
The Ribonuclease P database, Nucleic Acids Research, vol.22, issue.17, pp.3660-3662, 1994. ,
DOI : 10.1093/nar/22.17.3660
Prediction of complete gene structures in human genomic DNA, Journal of Molecular Biology, vol.268, issue.1, pp.78-94, 1997. ,
Descrambling DSCAM Diversity, Cell, vol.125, issue.3, pp.421-424, 2006. ,
DOI : 10.1016/j.cell.2006.04.012
URL : http://doi.org/10.1016/j.cell.2006.04.012
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner, Genome Research, vol.14, issue.4, pp.708-723, 2004. ,
DOI : 10.1101/gr.1933104
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization, BMC Bioinformatics, vol.8, issue.1, p.271, 2007. ,
DOI : 10.1186/1471-2105-8-271
Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database, Nucleic Acids Research, vol.24, issue.8, pp.1395-1403, 1996. ,
DOI : 10.1093/nar/24.8.1395
dbEST ? database for " expressed sequence tags, Nature Genetics, vol.4, pp.332-33310, 1993. ,
Comparative Analysis and Application to Exon Prediction, Genome Research, vol.10, issue.7, pp.950-958, 2000. ,
Human and mouse gene structure : comparative analysis and application to exon prediction, Proceedings of the 4th Annual International Conference on Computational Molecular Biology RECOMB, pp.46-53, 2000. ,
RNA modeling using stochastic context-free grammars, 1999. ,
Orphan gene finding???an exon assembly approach, Theoretical Computer Science, vol.290, issue.3, pp.1407-143110, 2003. ,
DOI : 10.1016/S0304-3975(02)00043-9
URL : https://hal.archives-ouvertes.fr/hal-00427367
How to Compare Arc-Annotated Sequences : The Alignment Hierarchy, In String Processing and Information Retrieval (SPIRE) Lecture Notes in Computer Science, vol.4209, pp.291-30310, 2006. ,
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences, Bioinformatics, vol.20, issue.17, pp.2911-2917, 2004. ,
FastR : fast database search tool for noncoding RNA, Proceedings of the IEEE Computer Society Bioinformatics Conference, pp.52-61, 2004. ,
NONCODE : an integrated knowledge database of non-coding RNAs, Nucleic Acids Research, vol.33, pp.112-115, 2005. ,
A computational approach to identify genes for functional RNAs in genomic sequences, Nucleic Acids Research, vol.29, issue.19, pp.3928-3938, 2001. ,
DOI : 10.1093/nar/29.19.3928
Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency, RNA, vol.11, issue.5, pp.578-591, 2005. ,
DOI : 10.1261/rna.7220505
Inferring consensus structure from nucleic acid sequences, Computational Applications in Biosciences, vol.7, issue.3, pp.347-352, 1991. ,
MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure, Proceedings of the National Academy of Sciences of the United States of America, pp.12102-12107, 2004. ,
DOI : 10.1073/pnas.0404193101
Multiple sequence alignment with hierarchical clustering, Nucleic Acids Research, vol.16, issue.22, pp.10881-10890, 1988. ,
DOI : 10.1093/nar/16.22.10881
Reference based annotation with Gene- Mapper, Genome Biology, vol.7, issue.R29, pp.10-1186, 2006. ,
NORINE : a database of nonribosomal peptides, Nucleic Acids Research, 2007. ,
Central Dogma of Molecular Biology, Nature, vol.215, issue.5258, pp.561-563, 1970. ,
DOI : 10.1038/227561a0
The high spontaneous mutation rate: Is it a health risk?, Proceedings of the National Academy of Sciences, vol.94, issue.16, pp.8380-8386, 1997. ,
DOI : 10.1073/pnas.94.16.8380
The Ribosomal Database Project : improved alignments and new tools for rRNA analysis, Nucleic Acids Research, vol.37, pp.141-145, 2009. ,
ddbRNA: detection of conserved secondary structures in multiple alignments, Bioinformatics, vol.19, issue.13, pp.1606-1611, 2003. ,
DOI : 10.1093/bioinformatics/btg229
Identifying bacterial genes and endosymbiont DNA with Glimmer, Bioinformatics, vol.23, issue.6, pp.673-679, 2007. ,
Rates of Spontaneous Mutation, Genetics, vol.148, pp.1667-1686, 1998. ,
Sfold web server for statistical folding and rational design of nucleic acids, Nucleic Acids Research, vol.32, issue.Web Server, pp.135-176, 2004. ,
DOI : 10.1093/nar/gkh449
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints, BMC Bioinformatics, vol.7, issue.400, pp.10-1186, 2006. ,
Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids, 1999. ,
DOI : 10.1017/CBO9780511790492
Improved microbial gene identification with GLIMMER, Nucleic Acids Research, vol.27, issue.23, pp.4636-4641, 1999. ,
A Bayesian statistical algorithm for RNA secondary structure prediction, Computers & Chemistry, vol.23, issue.3-4, pp.387-400, 1999. ,
DOI : 10.1016/S0097-8485(99)00010-8
Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond, Nucleic Acids Research, vol.29, issue.5, pp.1034-1046, 2001. ,
DOI : 10.1093/nar/29.5.1034
A statistical sampling algorithm for RNA secondary structure prediction, Nucleic Acids Research, vol.31, issue.24, pp.7280-7301, 2003. ,
DOI : 10.1093/nar/gkg938
Searching for patterns in genomic data, Trends in Genetics, vol.13, issue.12, pp.497-49810, 1997. ,
DOI : 10.1016/S0168-9525(97)01347-4
Gene Structure Prediction by Linguistic Methods, Genomics, vol.23, issue.3, pp.540-551, 1994. ,
DOI : 10.1006/geno.1994.1541
CONTRAfold : RNA secondary structure prediction without physics-based models, Bioinformatics, vol.22, issue.14, pp.90-98, 2006. ,
STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time, Bioinformatics, vol.22, issue.13, pp.1593-1599, 2006. ,
DOI : 10.1093/bioinformatics/btl142
RNA sequence analysis using covariance models, Nucleic Acids Research, vol.22, issue.11, pp.2079-2088, 1994. ,
Non???coding RNA genes and the modern RNA world, Nature Reviews Genetics, vol.10, issue.12, pp.919-92910, 2001. ,
DOI : 10.1038/35103511
Algorithmes pour la prédiction de structures secondaires d'ARN, 2006. ,
Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences, BMC Bioinformatics, vol.8, issue.1, p.464, 2007. ,
DOI : 10.1186/1471-2105-8-464
URL : https://hal.archives-ouvertes.fr/hal-00361249
Exploring genomic dark matter : a critical assessment of the performance of homology search methods on noncoding RNA, Genome Research, vol.17, issue.1, pp.117-125, 2007. ,
MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences, Nucleic Acids Research, vol.36, issue.Web Server, pp.14-18, 2008. ,
DOI : 10.1093/nar/gkn321
URL : https://hal.archives-ouvertes.fr/hal-00823594
MPFR, ACM Transactions on Mathematical Software, vol.33, issue.2, p.13, 2007. ,
DOI : 10.1145/1236463.1236468
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers, Journal of Computational Biology, vol.7, issue.1-2, pp.171-18210, 2000. ,
DOI : 10.1089/10665270050081441
A computer program for aligning a cDNA sequence with a genomic DNA sequence, Genome Research, vol.8, issue.9, pp.967-974, 1998. ,
ORFs and Genes: How Strong a Connection?, Journal of Computational Biology, vol.2, issue.1, pp.117-123, 1995. ,
DOI : 10.1089/cmb.1995.2.117
Pfam: clans, web tools and services, Nucleic Acids Research, vol.34, issue.90001, pp.247-251, 2006. ,
DOI : 10.1093/nar/gkj149
Prediction of human cDNA from its homologous mouse full-length cDNA and human shotgun database, FEBS Letters, vol.6, issue.3, pp.129-132, 1999. ,
DOI : 10.1016/S0014-5793(99)01696-8
Assessment of protein coding measures, Nucleic Acids Research, vol.20, issue.24, pp.6441-6450, 1992. ,
Computational identification of protein-coding sequences by comparative analysis, Proceedings of the 1st IEEE, pp.95-102, 2007. ,
Computational identification of proteincoding sequences by comparative analysis, International Journal of Data Mining and Bioinformatics, 2009. ,
Recoding: Dynamic Reprogramming of Translation, Annual Review of Biochemistry, vol.65, issue.1, pp.741-768, 1996. ,
DOI : 10.1146/annurev.bi.65.070196.003521
Using multiple alignments to improve gene prediction, Journal of Computational Biology, vol.13, issue.2, pp.379-393, 2006. ,
Engineering a software tool for gene structure prediction in higher organisms . Information and Software Technology, pp.47965-978, 2005. ,
Prediction of function in DNA sequence analysis, Journal of Computational Biology, vol.2, issue.1, pp.87-115, 1995. ,
Codon usage in bacteria: correlation with gene expressivity, Nucleic Acids Research, vol.10, issue.22, pp.7055-7074, 1982. ,
DOI : 10.1093/nar/10.22.7055
URL : https://hal.archives-ouvertes.fr/hal-00697906
A comprehensive comparison of comparative RNA structure prediction approaches, BMC Bioinformatics, vol.5, issue.140, 2004. ,
Codon frequencies in 119 individual genes confirm corsistent choices of degenerate bases according to genome type, Nucleic Acids Research, vol.8, issue.9, pp.1893-1912, 1980. ,
DOI : 10.1093/nar/8.9.1893
RNA modeling using Gibbs sampling and stochastic context free grammars, Proceedings of the 2nd International Conference on Intelligent Systems for Molecular Biology ISMB, pp.138-146, 1994. ,
Darwin v. 2.0 : an interpreted computer language for the biosciences, Bioinformatics, vol.16, issue.2, pp.101-103, 2000. ,
Rfam: an RNA family database, Nucleic Acids Research, vol.31, issue.1, pp.439-441, 2003. ,
DOI : 10.1093/nar/gkg006
miRBase: microRNA sequences, targets and gene nomenclature, Nucleic Acids Research, vol.34, issue.90001, pp.140-144, 2006. ,
DOI : 10.1093/nar/gkj112
Rfam, Nucleic Acids Research Journal of Molecular Biology, vol.25, issue.5, pp.121-124, 2001. ,
DOI : 10.1002/9780471650126.dob1069
PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences, Nucleic Acids Research, vol.31, issue.13, pp.313608-3612, 2003. ,
DOI : 10.1093/nar/gkg548
Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA, Bioinformatics, vol.6, issue.4, pp.325-331, 1990. ,
DOI : 10.1093/bioinformatics/6.4.325
Gene recognition via spliced sequence alignment, Proceedings of the National Academy of Sciences of the United States of America, pp.9061-9066, 1996. ,
Evaluating plague and smallpox as historical selective pressures for the CCR5-??32 HIV-resistance allele, Proceedings of the National Academy of Sciences, vol.100, issue.25, pp.15276-15279, 2003. ,
DOI : 10.1073/pnas.2435085100
Assembling Genes from Predicted Exons in Linear Time with Dynamic Programming, Journal of Computational Biology, vol.5, issue.4, pp.681-702, 1998. ,
DOI : 10.1089/cmb.1998.5.681
Statistics of extremes, 1958. ,
Dinucleotide controlled null models for comparative RNA gene prediction, BMC Bioinformatics, vol.9, issue.1, pp.24810-1186, 2008. ,
DOI : 10.1186/1471-2105-9-248
URL : http://doi.org/10.1186/1471-2105-9-248
A benchmark of multiple sequence alignment programs upon structural RNAs, Nucleic Acids Research, vol.33, issue.8, pp.2433-2439, 2005. ,
A Tool for Analyzing and Annotating Genomic Sequences, Genomics, vol.46, issue.1, pp.37-45, 1997. ,
DOI : 10.1006/geno.1997.4984
The Ensembl genome database project, Nucleic Acids Research, vol.30, issue.1, pp.38-41, 2002. ,
Alignment of RNA base pairing probability matrices, Bioinformatics, vol.20, issue.14, pp.2222-2227, 2004. ,
Fast folding and comparison of RNA secondary structures, Monatshefte für Chemie, vol.125, pp.167-188, 1994. ,
Secondary structure prediction for aligned RNA sequences, Journal of Molecular Biology, vol.319, issue.502, pp.1059-106610, 2002. ,
Assessing the reliability of RNA folding using statistical mechanics, Journal of Molecular Biology, vol.267, issue.5, pp.1104-1112, 1997. ,
DOI : 10.1006/jmbi.1997.0889
Amino acid substitution matrices from protein blocks., Proceedings of the National Academy of Sciences, vol.89, issue.22, pp.10915-109191036, 1992. ,
DOI : 10.1073/pnas.89.22.10915
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC50453/pdf
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search, Nucleic Acids Research, vol.33, issue.Web Server, pp.650-653, 2005. ,
DOI : 10.1093/nar/gki473
Accelerated probabilistic inference of RNA structure evolution, BMC Bioinformatics, vol.6, pp.7310-1186, 2005. ,
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign, BMC Bioinformatics, vol.8, issue.1, p.130, 2007. ,
DOI : 10.1186/1471-2105-8-130
Non-coding RNAs: hope or hype?, Trends in Genetics, vol.21, issue.5, pp.289-297, 2005. ,
DOI : 10.1016/j.tig.2005.03.007
Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix Local similarity in RNA secondary structures, Proceedings of the IEEE Computer Society Bioinformatics Conference, pp.1896-1908159, 2003. ,
Pure multiple RNA secondary structure alignments: a progressive profile approach, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.1, issue.1, pp.53-62, 2004. ,
DOI : 10.1109/TCBB.2004.11
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes, Journal of Molecular Biology, vol.146, issue.1, pp.1-21, 1981. ,
DOI : 10.1016/0022-2836(81)90363-6
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system, Journal of Molecular Biology, vol.151, issue.3, pp.389-409, 1981. ,
DOI : 10.1016/0022-2836(81)90003-6
Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes, Journal of Molecular Biology, vol.158, issue.4, pp.573-597, 1982. ,
DOI : 10.1016/0022-2836(82)90250-9
Ribosomal frameshifting in retroviral gene expression, 1988. ,
EbEST: An Automated Tool Using Expressed Sequence Tags to Delineate Gene???Structure, Genome Research, vol.8, issue.3, pp.268-275, 1998. ,
DOI : 10.1101/gr.8.3.268
A General Edit Distance between RNA Structures, Journal of Computational Biology, vol.9, issue.2, pp.371-38810, 2002. ,
DOI : 10.1089/10665270252935511
Improved predictions of secondary structures for RNA., Proceedings of the National Academy of Sciences of the United States of America, pp.7706-7710, 1989. ,
DOI : 10.1073/pnas.86.20.7706
[17] Predicting optimal and suboptimal secondary structure for RNA, Methods in Enzymology, vol.183, pp.281-306, 1990. ,
DOI : 10.1016/0076-6879(90)83019-6
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
Chance and statistical significance in protein and DNA sequence analysis, Science, vol.257, issue.5066, pp.39-49, 1992. ,
DOI : 10.1126/science.1621093
The UCSC Genome Browser Database, Nucleic Acids Research, vol.31, issue.1, pp.51-54, 2003. ,
DOI : 10.1093/nar/gkg129
An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy, Nucleic Acids Research, vol.35, issue.1, pp.317-324, 2007. ,
DOI : 10.1093/nar/gkl1026
RSEARCH : Finding homologs of single structured RNA sequences, BMC Bioinformatics, vol.4, issue.1, p.44, 2003. ,
Integrating genomic homology into gene structure prediction, Bioinformatics, vol.17, issue.1, pp.140-148, 2001. ,
Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA, Nature Genetics, vol.7, issue.1, pp.48-5310, 1994. ,
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history, Bioinformatics, vol.15, issue.6, pp.446-454, 1999. ,
DOI : 10.1093/bioinformatics/15.6.446
Pfold: RNA secondary structure prediction using stochastic context-free grammars, Nucleic Acids Research, vol.31, issue.13, pp.3423-3428, 2003. ,
DOI : 10.1093/nar/gkg614
The UCSC Table Browser data retrieval tool, Nucleic Acids Research, vol.32, issue.90001, pp.493-496, 2004. ,
DOI : 10.1093/nar/gkh103
A generalized hidden Markov model for the recognition of human genes in DNA, Proceedings of the 4th International Conference on Intellignet Systems for Molecular Biology ISMB, pp.134-142, 1996. ,
Noncoding RNA genes identified in AT-rich hyperthermophiles, Proceedings of the National Academy of Sciences, vol.99, issue.11, pp.7542-7547, 2002. ,
DOI : 10.1073/pnas.112063799
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC124278
DNA, Nucleic Acids Research, vol.22, issue.22, pp.4768-4778, 1994. ,
DOI : 10.1093/nar/22.22.4768
Counts of long aligned word matches among random letter sequences, Advances in Applied Probability, vol.26, issue.02, pp.293-351, 1987. ,
DOI : 10.1073/pnas.80.18.5660
Maximal Length of Common Words Among Random Letter Sequences, The Annals of Probability, vol.16, issue.2, pp.535-563, 1988. ,
DOI : 10.1214/aop/1176991772
PAGAN : Predict and Annotate Genes in genomic sequence based on ANalysis of EST Clusters, International Conference on Intellignet Systems for Molecular Biology ISMB, 2001. ,
SCOR : a structural classification of RNA database, Nucleic Acids Research, vol.30, issue.1, pp.392-394, 2002. ,
Murlet: a practical multiple alignment tool for structural RNA sequences, Bioinformatics, vol.23, issue.13, pp.1588-1598, 2007. ,
DOI : 10.1093/bioinformatics/btm146
fRNAdb : a platform for mining/annotating functional RNA candidates from non-coding RNA sequences, Database issue) :D145?D148, 2007. ,
hmm : new solution for gene finding, Nucleic Acids Research, vol.26, issue.4, pp.1107-1115, 1998. ,
The ERPIN server: an interface to profile-based RNA motif identification, Nucleic Acids Research, vol.32, issue.Web Server, pp.160-165, 2004. ,
DOI : 10.1093/nar/gkh418
An RNA pattern matching program with enhanced performance and portability, Bioinformatics, vol.10, issue.2, pp.211-212, 1994. ,
DOI : 10.1093/bioinformatics/10.2.211
Computing expectation values for RNA motifs using discrete convolutions, BMC Bioinformatics, vol.6, pp.11810-1186, 2005. ,
URL : https://hal.archives-ouvertes.fr/inserm-00090525
Genomic sequence comparison of the human and mouse XRCC1 DNA repair gene regions, Genomics, vol.25, issue.2, pp.547-554, 1995. ,
DOI : 10.1016/0888-7543(95)80056-R
An algorithm for detecting homologues of known structured rnas in genomes, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004., pp.300-310, 2004. ,
DOI : 10.1109/CSB.2004.1332443
Rapid and sensitive protein similarity searches, Science, vol.227, issue.4693, pp.1435-1441, 1985. ,
Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus, Proceedings of the National Academy of Sciences of the United States of America, issue.11, pp.765495-5499, 1979. ,
Gene identification in novel eukaryotic genomes by self-training algorithm, Nucleic Acids Research, vol.33, issue.20, pp.6494-6506, 2005. ,
DOI : 10.1093/nar/gki937
Geometric nomenclature and classification of RNA base pairs, RNA, vol.7, issue.4, pp.499-512, 2001. ,
A method for aligning RNA secondary structures and its application to RNA motif detection, BMC Bioinformatics, vol.6, pp.8910-1186, 2005. ,
Fast evaluation of internal loops in RNA secondary structure prediction, Bioinformatics, vol.15, issue.6, pp.440-445, 1999. ,
Confidence in comparative genomics, Genome Research, vol.18, issue.2, pp.199-200, 2008. ,
Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences, Proceedings of the National Academy of Sciences of the United States of America, pp.959407-9412, 1998. ,
DOI : 10.1073/pnas.95.16.9407
The equilibrium partition function and base pair binding probabilities for RNA secondary structure, Biopolymers, vol.24, issue.6-7, pp.6-71105, 1990. ,
DOI : 10.1002/bip.360290621
Gene structure conservation aids similarity based gene prediction, Nucleic Acids Research, vol.32, issue.2, pp.776-783, 2004. ,
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proceedings of the National Academy of Sciences, vol.101, issue.19, pp.7287-7292, 2004. ,
DOI : 10.1073/pnas.0401799101
RNAMotif, an RNA secondary structure definition and search algorithm, Nucleic Acids Research, vol.29, issue.22, pp.4724-4735, 2001. ,
DOI : 10.1093/nar/29.22.4724
Eukaryotic ribosomal RNA : the recent excitement in the nucleotide modification problem, Chromosoma, vol.105, issue.78, pp.391-400, 1997. ,
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
Current methods of gene prediction, their strengths and weaknesses, Nucleic Acids Research, vol.30, issue.19, pp.4103-4117, 2002. ,
DOI : 10.1093/nar/gkf543
URL : https://hal.archives-ouvertes.fr/hal-00427288
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, Journal of Molecular Biology, vol.288, issue.5, pp.911-940, 1999. ,
DOI : 10.1006/jmbi.1999.2700
Dynalign : an algorithm for finding the secondary structure common to two RNA sequences, Journal of Molecular Biology, vol.317, issue.2, pp.191-203, 2002. ,
PatternHunter: faster and more sensitive homology search, Bioinformatics, vol.18, issue.3, pp.440-445, 2002. ,
DOI : 10.1093/bioinformatics/18.3.440
R-Coffee: a web server for accurately aligning noncoding RNA sequences, Nucleic Acids Research, vol.36, issue.Web Server, pp.10-13, 2008. ,
DOI : 10.1093/nar/gkn278
The Functional RNA Database 3.0 : databases to support mining and annotation of functional RNAs Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences, Nucleic Acids Research Genome Research, vol.6, issue.9, pp.846-857, 1996. ,
Query-dependent banding (QDB) for faster RNA similarity searches, PLoS Computational Biology, vol.3, issue.3, p.56, 2007. ,
Gene recognition in eukaryotic DNA by comparison of genomic sequences, Bioinformatics, vol.17, issue.11, pp.1011-1018, 2001. ,
DOI : 10.1093/bioinformatics/17.11.1011
T-coffee: a novel method for fast and accurate multiple sequence alignment, Journal of Molecular Biology, vol.302, issue.1, pp.205-217, 2000. ,
DOI : 10.1006/jmbi.2000.4042
Fast algorithm for predicting the secondary structure of single-stranded RNA., Proceedings of the National Academy of Sciences of the United States of America, pp.6309-6313, 1980. ,
DOI : 10.1073/pnas.77.11.6309
YASS: enhancing the sensitivity of DNA similarity search, Nucleic Acids Research, vol.33, issue.Web Server, pp.540-543, 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
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. ,
Analysis of internal loops within the RNA secondary structure in almost quadratic time, Bioinformatics, vol.22, issue.11, pp.1317-1324, 2006. ,
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome, PLoS Computational Biology, vol.100, issue.4, p.33, 2006. ,
DOI : 10.1371/journal.pcbi.0020033.st004
Approche algorithmique de la prédiction de structures secondaires, 2003. ,
Gene finding with a hidden Markov model of genome structure and evolution, Bioinformatics, vol.19, issue.2, pp.219-227, 2003. ,
DOI : 10.1093/bioinformatics/19.2.219
PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance, Bioinformatics, vol.16, issue.5, pp.439-450, 2000. ,
DOI : 10.1093/bioinformatics/16.5.439
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data, Nature, vol.349, issue.7183, pp.45251-55, 2008. ,
DOI : 10.1038/nature06684
RNAdb 2.0--an expanded database of mammalian non-coding RNAs, Nucleic Acids Research, vol.35, issue.Database, pp.178-82, 2007. ,
DOI : 10.1093/nar/gkl926
RNAdb--a comprehensive mammalian noncoding RNA database, Nucleic Acids Research, vol.33, issue.Database issue, pp.125-155, 2005. ,
DOI : 10.1093/nar/gki089
Finding the common structure shared by two homologous RNAs, Bioinformatics, vol.19, issue.1, pp.108-116, 2003. ,
DOI : 10.1093/bioinformatics/19.1.108
Combinatorial approaches to gene recognition, Computers and Chemistry, vol.21, issue.4, pp.229-235, 1997. ,
Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences, Gene, vol.226, issue.1, pp.126-137, 1999. ,
DOI : 10.1016/S0378-1119(98)00509-5
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
Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs, Bioinformatics, vol.16, issue.7, pp.583-605, 2000. ,
DOI : 10.1093/bioinformatics/16.7.583
Noncoding RNA gene detection using comparative sequence analysis, BMC Bioinformatics, issue.2, 2001. ,
Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction, Bioinformatics, vol.21, issue.17, pp.3516-3523, 2005. ,
DOI : 10.1093/bioinformatics/bti577
Computational identification of noncoding RNAs in E. coli by comparative genomics, Current Biology, vol.11, issue.17, pp.1369-1373, 2001. ,
DOI : 10.1016/S0960-9822(01)00401-8
Gene structure prediction using information on homologous protein sequence, Bioinformatics, vol.12, issue.3, pp.161-170, 1996. ,
DOI : 10.1093/bioinformatics/12.3.161
Evaluation of Gene-Finding Programs on Mammalian Sequences, Genome Research, vol.11, issue.5, pp.817-832, 2001. ,
DOI : 10.1101/gr.147901
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows, Nucleic Acids Research, vol.35, issue.Web Server, pp.320-324, 2007. ,
DOI : 10.1093/nar/gkm258
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots, Bioinformatics, vol.20, issue.1, pp.58-66, 2004. ,
DOI : 10.1093/bioinformatics/btg373
ILM: a web server for predicting RNA secondary structures with pseudoknots, Nucleic Acids Research, vol.32, issue.Web Server, pp.146-155, 2004. ,
DOI : 10.1093/nar/gkh444
Fundamentals of Genetics and the Biology Place. Pearson Education, Limited, 1993. ,
MOLECULAR BIOLOGY: Glimpses of a Tiny RNA World, Science, vol.294, issue.5543, pp.797-799, 2001. ,
DOI : 10.1126/science.1066315
Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems, SIAM Journal on Applied Mathematics, vol.45, issue.5, pp.810-82510, 1985. ,
DOI : 10.1137/0145048
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons, Bioinformatics, vol.21, issue.16, pp.3352-3359, 2005. ,
DOI : 10.1093/bioinformatics/bti550
Dscam and DSCAM: complex genes in simple animals, complex animals yet simple genes, Genes & Development, vol.23, issue.2, pp.147-156, 2009. ,
DOI : 10.1101/gad.1752909
Microbial gene identification using interpolated Markov models, Nucleic Acids Research, vol.26, issue.2, pp.544-548, 1998. ,
The Linguistics of DNA, American Scientist, vol.80, pp.579-591, 1992. ,
Combined use of sequence similarity and codon bias for coding region identification, Journal of Computational Biology, vol.1, issue.1, pp.39-50, 1994. ,
Computational identification of evolutionarily conserved exons, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, pp.177-186, 2004. ,
DOI : 10.1145/974614.974638
Phylogenetic Hidden Markov Models, Statistical Methods in Molecular Evolution, pp.325-351 ,
DOI : 10.1007/0-387-27733-1_12
Codon preference and its use in identifying protein coding regions in long DNA sequences, Nucleic Acids Research, vol.10, issue.1, pp.141-156, 1982. ,
DOI : 10.1093/nar/10.1.141
Eug??ne: An Eukaryotic Gene Finder That Combines Several Sources of Evidence, Computational Biology, pp.111-125, 2001. ,
DOI : 10.1007/3-540-45727-5_10
Interpolated Markov models for eukaryotic gene finding, Genomics, vol.59, issue.1, pp.24-31, 1999. ,
Identification of protein coding regions in genomic DNA, Journal of Molecular Biology, vol.248, issue.1, pp.1-18, 1995. ,
Ab initio Gene Finding in Drosophila Genomic DNA, Genome Research, vol.10, issue.4, pp.516-522, 2000. ,
Gene Prediction with a Hidden Markov Model, 2003. ,
Consensus patterns in DNA, Methods in Enzymology, vol.183, pp.211-221, 1990. ,
RNAshapes: an integrated RNA analysis package based on abstract shapes, Bioinformatics, vol.22, issue.4, pp.500-503, 2006. ,
DOI : 10.1093/bioinformatics/btk010
Gene prediction with a hidden Markov model and a new intron submodel, Bioinformatics, vol.19, issue.Suppl 2, pp.215-225, 2003. ,
DOI : 10.1093/bioinformatics/btg1080
A fast algorithm for RNA secondary structure prediction including pseudoknots, Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings., pp.11-17, 2003. ,
DOI : 10.1109/BIBE.2003.1188924
P-DCFOLD OR HOW TO PREDICT ALL KINDS OF PSEUDOKNOTS IN RNA SECONDARY STRUCTURES, International Journal on Artificial Intelligence Tools, vol.14, issue.05, pp.703-71610, 2005. ,
DOI : 10.1142/S021821300500234X
URL : https://hal.archives-ouvertes.fr/hal-00343084
Automatic RNA secondary structure prediction with a comparative approach, Computers & Chemistry, vol.26, issue.5, pp.521-530, 2002. ,
DOI : 10.1016/S0097-8485(02)00012-8
URL : https://hal.archives-ouvertes.fr/hal-00427303
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
Multiple structural alignment and clustering of RNA sequences, Bioinformatics, vol.23, issue.8, pp.926-932, 2007. ,
DOI : 10.1093/bioinformatics/btm049
A fast structural multiple alignment method for long RNA sequences, BMC Bioinformatics, vol.9, issue.1, pp.3310-1186, 2008. ,
DOI : 10.1186/1471-2105-9-33
On splice site prediction using weight array models: a comparison of smoothing techniques, Journal of Physics: Conference Series, vol.90, issue.8pp, p.12004, 2007. ,
DOI : 10.1088/1742-6596/90/1/012004
Comparative analysis of RNA genes : the caRNAc software, Methods in Molecular Biology, vol.395, pp.465-474, 2007. ,
CARNAC : folding families of related RNAs, Nucleic Acids Research, vol.32, pp.142-147, 2004. ,
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs, Bioinformatics, vol.15, issue.1, pp.87-88, 1999. ,
DOI : 10.1093/bioinformatics/15.1.87
AGenDA: homology-based gene prediction, Bioinformatics, vol.19, issue.12, pp.1575-1577, 2003. ,
DOI : 10.1093/bioinformatics/btg181
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.672.6411
RNA Structure Prediction, Annual Review of Biophysics and Biophysical Chemistry, vol.17, issue.1, pp.167-192, 1988. ,
DOI : 10.1146/annurev.bb.17.060188.001123
SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments, Bioinformatics, vol.22, issue.14, pp.1723-1729, 2006. ,
DOI : 10.1093/bioinformatics/btl177
SARNA-Predict : A Simulated Annealing Algorithm for RNA Secondary Structure Prediction CIBCB '06, IEEE Symposium on, pp.1-10, 2006. ,
SARNA-Predict : A Study of RNA Secondary Structure Prediction Using Different Annealing Schedules, Computational Intelligence and Bioinformatics and Computational Biology CIBCB '07. IEEE Symposium on, pp.239-246, 2007. ,
Introduction to Mathematical Probability, pp.23-24, 1937. ,
Error bounds for convolutional codes and an asymptotically optimum decoding algorithm, IEEE Transactions on Information Theory, vol.13, issue.2, pp.260-269, 1967. ,
DOI : 10.1109/TIT.1967.1054010
Structural analysis of aligned RNAs, Nucleic Acids Research, vol.34, issue.19, pp.5471-5481, 2006. ,
DOI : 10.1093/nar/gkl692
Database resources of the National Center for Biotechnology Information PANDIT : an evolution-centric database of protein and associated nucleotide domains with inferred trees Complete suboptimal folding of RNA and the stability of secondary structures, Database issue D327?331, pp.13-21145, 1999. ,
Alternative splicing of Drosophila Dscam generates axon guidance receptors that exhibit isoform-specific homophilic binding SGP-1 : Prediction and Validation of Homologous Genes Based on Sequence Alignments Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics, Cell Genome Research Journal of Molecular Biology, vol.118, issue.3421, pp.619-6331574, 2001. ,
R-Coffee: a method for multiple alignment of non-coding RNA, Nucleic Acids Research, vol.36, issue.9, p.52, 2008. ,
DOI : 10.1093/nar/gkn174
From The Cover: Fast and reliable prediction of noncoding RNAs, Proceedings of the National Academy of Sciences of the United States of America, pp.2454-2459, 2005. ,
DOI : 10.1073/pnas.0409169102
An enhanced RNA alignment benchmark for sequence alignment programs, Algorithms for Molecular Biology, vol.1, pp.191748-7188, 2006. ,
Structured RNAs in the ENCODE selected regions of the human genome, Genome Research, vol.17, issue.6, pp.852-864, 2007. ,
DOI : 10.1101/gr.5650707
The European ribosomal RNA database, Nucleic Acids Research, vol.32, issue.90001, pp.101-103, 2004. ,
DOI : 10.1093/nar/gkh065
URL : https://hal.archives-ouvertes.fr/hal-00427639
Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy, Bioinformatics, vol.20, issue.Suppl 1, pp.334-375, 2004. ,
DOI : 10.1093/bioinformatics/bth925
Sequence-based heuristics for faster annotation of non-coding RNA families, Bioinformatics, vol.22, issue.1, pp.35-39, 2006. ,
DOI : 10.1093/bioinformatics/bti743
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering, PLoS Computational Biology, vol.22, issue.4, p.65, 2007. ,
DOI : 10.1371/journal.pcbi.0030065.sd001
Constructing gene models from accurately predicted exons: an application of dynamic programming, Bioinformatics, vol.10, issue.6, pp.613-623, 1994. ,
DOI : 10.1093/bioinformatics/10.6.613
Computational Inference of Homologous Gene Structures in the Human Genome, Genome Research, vol.11, issue.5, pp.803-816, 2001. ,
DOI : 10.1101/gr.175701
RDfolder: a web server for prediction of RNA secondary structure, Nucleic Acids Research, vol.32, issue.Web Server, pp.150-153, 2004. ,
DOI : 10.1093/nar/gkh445
CMfinder--a covariance model based RNA motif finding algorithm, Bioinformatics, vol.22, issue.4, pp.445-452, 2006. ,
DOI : 10.1093/bioinformatics/btk008
URL : http://bio.cs.washington.edu/yzizhen/CMfinder/appendix.pdf
DARN! A Weighted Constraint Solver for RNA Motif Localization, Constraints, vol.312, issue.2???3, pp.91-10910, 2008. ,
DOI : 10.1007/s10601-007-9033-9
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
RNA secondary structures and their prediction, Bulletin of Mathematical Biology, vol.9, issue.Suppl. 2, pp.591-621, 1984. ,
DOI : 10.1007/BF02459506
On finding all suboptimal foldings of an RNA molecule, Science, vol.244, issue.4900, pp.48-52, 1989. ,
DOI : 10.1126/science.2468181
Localisation d'ARN non-codants par réseaux de contraintes pondérées, 2007. ,