C. Alkan, RNA???RNA Interaction Prediction and Antisense RNA Target Search, Journal of Computational Biology, vol.13, issue.2, pp.267-282, 2006.
DOI : 10.1089/cmb.2006.13.267

S. Altuvia, Identification of bacterial small non-coding RNAs: experimental approaches, Current Opinion in Microbiology, vol.10, issue.3, pp.257-261, 2007.
DOI : 10.1016/j.mib.2007.05.003

M. Antal, A Small Bacterial RNA Regulates a Putative ABC Transporter, Journal of Biological Chemistry, vol.280, issue.9, pp.7901-7908, 2005.
DOI : 10.1074/jbc.M413071200

URL : https://hal.archives-ouvertes.fr/hal-00196808

L. Argaman, Novel small RNA-encoding genes in the intergenic regions of Escherichia coli, Current Biology, vol.11, issue.12, pp.941-950, 2001.
DOI : 10.1016/S0960-9822(01)00270-6

I. Axmann, Identification of cyanobacterial non-coding RNAs by comparative genome analysis, Genome Biology, vol.6, issue.9, p.73, 2005.
DOI : 10.1186/gb-2005-6-9-r73

T. Babak, Considerations in the identification of functional RNA structural elements in genomic alignments, BMC Bioinformatics, vol.8, issue.1, p.33, 2007.
DOI : 10.1186/1471-2105-8-33

P. Babitzke and T. Romeo, CsrB sRNA family: sequestration of RNA-binding regulatory proteins, Current Opinion in Microbiology, vol.10, issue.2, pp.156-163, 2007.
DOI : 10.1016/j.mib.2007.03.007

S. Boisset, Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism, Genes & Development, vol.21, issue.11, pp.1353-1366, 2007.
DOI : 10.1101/gad.423507

URL : https://hal.archives-ouvertes.fr/hal-00167517

R. Carter, 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

S. Chen, A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome, Biosystems, vol.65, issue.2-3, pp.157-177, 2002.
DOI : 10.1016/S0303-2647(02)00013-8

S. Chen, MicC, a Second Small-RNA Regulator of Omp Protein Expression in Escherichia coli, Journal of Bacteriology, vol.186, issue.20, pp.6689-6697, 2004.
DOI : 10.1128/JB.186.20.6689-6697.2004

P. Clote, 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

A. Coventry, MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure, Proc. Natl Acad. Sci. USA, pp.12102-12107, 2004.
DOI : 10.1073/pnas.0404193101

C. Del-val, Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics, Molecular Microbiology, vol.67, issue.5, pp.1080-1091, 2007.
DOI : 10.1046/j.1365-2958.2003.03734.x

D. Di-bernardo, ddbRNA: detection of conserved secondary structures in multiple alignments, Bioinformatics, vol.19, issue.13, pp.1606-1611, 2003.
DOI : 10.1093/bioinformatics/btg229

V. Douchin, Down-regulation of Porins by a Small RNA Bypasses the Essentiality of the Regulated Intramembrane Proteolysis Protease RseP in Escherichia coli, Journal of Biological Chemistry, vol.281, issue.18, pp.12253-12259, 2006.
DOI : 10.1074/jbc.M600819200

G. A. Fichant and C. Burks, Identifying potential tRNA genes in genomic DNA sequences, Journal of Molecular Biology, vol.220, issue.3, pp.659-671, 1991.
DOI : 10.1016/0022-2836(91)90108-I

S. Griffiths-jones, Rfam: annotating non-coding RNAs in complete genomes, Nucleic Acids Research, vol.33, issue.Database issue, pp.121-124, 2005.
DOI : 10.1093/nar/gki081

A. R. Gruber, The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures, Nucleic Acids Research, vol.35, issue.Web Server, pp.335-338, 2007.
DOI : 10.1093/nar/gkm222

S. Gottesman, Small RNA Regulators and the Bacterial Response to Stress, Cold Spring Harbor Symposia on Quantitative Biology, vol.58, issue.0, pp.1-11, 2006.
DOI : 10.1046/j.1365-2958.2003.03734.x

L. D. Hurst and A. R. Merchant, High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes, Proceedings of the Royal Society B: Biological Sciences, vol.268, issue.1466, pp.493-497, 2001.
DOI : 10.1098/rspb.2000.1397

A. Hüttenhofer and J. Vogel, Experimental approaches to identify non-coding RNAs, Nucleic Acids Research, vol.34, issue.2, pp.635-646, 2006.
DOI : 10.1093/nar/gkj469

S. Kang, CONSORF: a consensus prediction system for prokaryotic coding sequences, Bioinformatics, vol.23, issue.22, pp.3088-3090, 2007.
DOI : 10.1093/bioinformatics/btm512

R. J. Klein, Noncoding RNA genes identified in AT-rich hyperthermophiles, Proc. Natl Acad. Sci. USA, pp.7542-7547, 2002.
DOI : 10.1073/pnas.112063799

A. Lambert, 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

URL : http://doi.org/10.1093/nar/gkh418

D. Laslett and B. Canback, ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences, Nucleic Acids Research, vol.32, issue.1, pp.11-16, 2004.
DOI : 10.1093/nar/gkh152

J. Livny, sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes, Nucleic Acids Research, vol.33, issue.13, pp.4096-4105, 2005.
DOI : 10.1093/nar/gki715

J. Livny and M. K. Waldor, Identification of small RNAs in diverse bacterial species, Current Opinion in Microbiology, vol.10, issue.2, pp.96-101, 2007.
DOI : 10.1016/j.mib.2007.03.005

T. M. Lowe and S. R. Eddy, tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence, Nucleic Acids Research, vol.25, issue.5, pp.955-964, 1997.
DOI : 10.1093/nar/25.5.0955

T. J. Macke, 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

URL : http://doi.org/10.1093/nar/29.22.4724

P. Mandin, Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets, Nucleic Acids Research, vol.35, issue.3, pp.962-974, 2007.
DOI : 10.1093/nar/gkl1096

URL : https://hal.archives-ouvertes.fr/hal-00129258

E. Massé, Effect of RyhB Small RNA on Global Iron Use in Escherichia coli, Journal of Bacteriology, vol.187, issue.20, pp.6962-6971, 2005.
DOI : 10.1128/JB.187.20.6962-6971.2005

U. Mückstein, Thermodynamics of RNA-RNA binding, Bioinformatics, vol.22, issue.10, pp.1177-1182, 2006.
DOI : 10.1093/bioinformatics/btl024

Y. Ostberg, The Etiological Agent of Lyme Disease, Borrelia burgdorferi, Appears To Contain Only a Few Small RNA Molecules, Journal of Bacteriology, vol.186, issue.24, pp.8472-8477, 2004.
DOI : 10.1128/JB.186.24.8472-8477.2004

C. Pichon and B. Felden, Intergenic sequence inspector: searching and identifying bacterial RNAs, Bioinformatics, vol.19, issue.13, pp.1707-1709, 2003.
DOI : 10.1093/bioinformatics/btg235

URL : https://hal.archives-ouvertes.fr/inserm-00714226

C. Pichon and B. Felden, Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains, Proc. Natl Acad. Sci. USA, pp.14249-14254, 2005.
DOI : 10.1073/pnas.0503838102

URL : https://hal.archives-ouvertes.fr/inserm-00713114

C. Pichon and B. Felden, Proteins that interact with bacterial small RNA regulators, FEMS Microbiology Reviews, vol.31, issue.5, pp.614-625, 2007.
DOI : 10.1111/j.1574-6976.2007.00079.x

URL : https://hal.archives-ouvertes.fr/inserm-00712150

M. Regalia, Prediction of signal recognition particle RNA genes, Nucleic Acids Research, vol.30, issue.15, pp.3368-3377, 2002.
DOI : 10.1093/nar/gkf468

M. Rehmsmeier, Fast and effective prediction of microRNA/target duplexes, RNA, vol.10, issue.10, pp.1507-1517, 2004.
DOI : 10.1261/rna.5248604

E. Rivas and S. R. Eddy, 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

E. Rivas and S. Eddy, Noncoding RNA gene detection using comparative sequence analysis, BMC Bioinformatics, issue.2 8, 2001.

E. Rivas, 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

P. Schattner, Searching for RNA genes using base-composition statistics, Nucleic Acids Research, vol.30, issue.9, pp.2076-2082, 2002.
DOI : 10.1093/nar/30.9.2076

G. Storz and S. Gottesman, Versatile roles of small RNA regulators in bacteria, The RNA World, pp.567-594, 2006.

B. Tjaden, Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays, Nucleic Acids Research, vol.30, issue.17, pp.3732-3738, 2002.
DOI : 10.1093/nar/gkf505

B. Tjaden, Target prediction for small, noncoding RNAs in bacteria, Nucleic Acids Research, vol.34, issue.9, pp.2791-2802, 2006.
DOI : 10.1093/nar/gkl356

K. I. Udekwu, Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA, Genes & Development, vol.19, issue.19, pp.2355-2366, 2005.
DOI : 10.1101/gad.354405

A. Uzilov, Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change, BMC Bioinformatics, vol.7, issue.1, pp.173-203, 2006.
DOI : 10.1186/1471-2105-7-173

J. Vogel, RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria, Nucleic Acids Research, vol.31, issue.22, pp.6435-6443, 2003.
DOI : 10.1093/nar/gkg867

J. Vogel and C. M. Sharma, How to find small non-coding RNAs in bacteria, Biological Chemistry, vol.386, issue.12, pp.1219-1238, 2005.
DOI : 10.1515/BC.2005.140

J. Vogel and E. G. Wagner, Target identification of small noncoding RNAs in bacteria, Current Opinion in Microbiology, vol.10, issue.3, pp.262-270, 2007.
DOI : 10.1016/j.mib.2007.06.001

S. Washietl, Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome, Nature Biotechnology, vol.33, issue.11, pp.1383-1390, 2005.
DOI : 10.1126/science.1083423

S. Washietl, From The Cover: Fast and reliable prediction of noncoding RNAs, Proc. Natl Acad. Sci. USA, pp.2454-2459, 2005.
DOI : 10.1073/pnas.0409169102

K. M. Wassarman, Small RNAs in Escherichia coli, Trends in Microbiology, vol.7, issue.1, pp.37-45, 1999.
DOI : 10.1016/S0966-842X(98)01379-1

K. Wassarman, Identification of novel small RNAs using comparative genomics and microarrays, Genes & Development, vol.15, issue.13, pp.1637-1651, 2001.
DOI : 10.1101/gad.901001

N. Yachie, Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model, Gene, vol.372, pp.171-181, 2006.
DOI : 10.1016/j.gene.2005.12.034

A. Zhang, Global analysis of small RNA and mRNA targets of Hfq, Molecular Microbiology, vol.9, issue.4, pp.1111-1124, 2003.
DOI : 10.1046/j.1365-2958.2003.03734.x

M. Zuker, On finding all suboptimal foldings of an RNA molecule, Science, vol.244, issue.4900, pp.48-52, 1989.
DOI : 10.1126/science.2468181