S. Chen, E. A. Lesnik, T. A. Hall, R. Sampath, R. H. Griffey et al., 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. R. Eddy, Computational Genomics of Noncoding RNA Genes, Cell, vol.109, issue.2, pp.137-140, 2002.
DOI : 10.1016/S0092-8674(02)00727-4

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

A. Hüttenhofer, M. Kiefmann, S. Meier-ewert, J. O-'brien, H. Lehrang et al., RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse, The EMBO Journal, vol.20, issue.11, pp.2943-2953, 2001.
DOI : 10.1093/emboj/20.11.2943

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

E. Lesnik, R. Sampath, H. Levene, T. Henderson, J. Mcneil et al., Prediction of rho-independent transcriptional terminators in Escherichia coli, Nucleic Acids Research, vol.29, issue.17, pp.3583-3594, 2001.
DOI : 10.1093/nar/29.17.3583

F. Lisacek, Y. Diaz, and F. Michel, Automatic Identification of Group I Intron Cores in Genomic DNA Sequences, Journal of Molecular Biology, vol.235, issue.4, pp.1206-1217, 1994.
DOI : 10.1006/jmbi.1994.1074

T. M. Lowe and S. R. Eddy, A Computational Screen for Methylation Guide snoRNAs in Yeast, Science, vol.283, issue.5405, pp.1168-1171, 1999.
DOI : 10.1126/science.283.5405.1168

E. Rivas and S. R. Eddy, Noncoding RNA gene detection using comparative sequence analysis, BMC Bioinformatics, vol.2, issue.8, pp.1-19, 2001.

K. Wassarman, F. Repoila, C. Rosenow, G. Storz, and S. Gottesman, 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

K. Wassarman, Small RNAs in Bacteria, Cell, vol.109, issue.2, pp.141-144, 2002.
DOI : 10.1016/S0092-8674(02)00717-1

T. Yada, M. Nakao, . Totoki, and K. Nakai, Modeling and predicting transcriptional units of <$O_SSF>Escherichia coli<$C_SSF>genes using hidden Markov models, Bioinformatics, vol.15, issue.12, pp.987-993, 1999.
DOI : 10.1093/bioinformatics/15.12.987