M. Horn, A. Krogh, M. Brown, I. Mian, K. Sjölander et al., Chlamydiae as symbionts in eukaryotes113-131. 2. functional annotation with the Conserved Domain DatabaseDatabase issue):D205-210. 53. Eddy SR: Profile hidden Markov models Hidden Markov models in computational biology. Applications to protein modeling, Annu Rev Microbiol Nucleic Acids Res Bioinformatics J Mol Biol, vol.62, issue.2355, pp.755-7631501, 1994.

W. Pirovano, K. Feenstra, and J. Heringa, PRALINETM: a strategy for improved multiple alignment of transmembrane proteins, Bioinformatics, vol.24, issue.4, pp.492-497, 2008.
DOI : 10.1093/bioinformatics/btm636

V. Brendel, P. Bucher, I. Nourbakhsh, B. Blaisdell, and S. Karlin, Methods and algorithms for statistical analysis of protein sequences., Proceedings of the National Academy of Sciences, vol.89, issue.6, pp.2002-2006, 1992.
DOI : 10.1073/pnas.89.6.2002

S. Montgomerie, J. Cruz, S. Shrivastava, D. Arndt, M. Berjanskii et al., PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation, Nucleic Acids Research, vol.36, issue.Web Server, pp.202-209, 1991.
DOI : 10.1093/nar/gkn255

M. Delorenzi and T. Speed, An HMM model for coiled-coil domains and a comparison with PSSM-based predictions, Bioinformatics, vol.18, issue.4, pp.617-625, 2002.
DOI : 10.1093/bioinformatics/18.4.617

R. Gautier, D. Douguet, B. Antonny, and G. Drin, HELIQUEST: a web server to screen sequences with specific ??-helical properties, Bioinformatics, vol.24, issue.18, pp.2101-2102, 2008.
DOI : 10.1093/bioinformatics/btn392

URL : https://hal.archives-ouvertes.fr/hal-00311956

M. Karpenahalli, A. Lupas, and J. Söding, TPRpred: a tool for prediction of TPR-, PPR-and SEL1-like repeats from protein sequences, 62. Bornberg-Bauer E, Rivals E, Vingron M: Computational approaches to identify leucine zippers, pp.262740-2746, 1998.

A. Allaoui, P. Sansonetti, and C. Parsot, MxiD, an outer membrane protein necessary for the secretion of the Shigella flexneri Ipa invasins, Molecular Microbiology, vol.17, issue.1, pp.59-68, 1993.
DOI : 10.1016/0378-1119(85)90120-9

R. Ménard, P. Sansonetti, and C. Parsot, Nonpolar mutagenesis of the ipa genes defines IpaB, IpaC, and IpaD as effectors of Shigella flexneri entry into epithelial cells., Journal of Bacteriology, vol.175, issue.18, pp.5899-5906, 1993.
DOI : 10.1128/jb.175.18.5899-5906.1993

C. Chen, D. Chen, J. Sharma, W. Cheng, Y. Zhong et al., The Hypothetical Protein CT813 Is Localized in the Chlamydia trachomatis Inclusion Membrane and Is Immunogenic in Women Urogenitally Infected with C. trachomatis, Infection and Immunity, vol.74, issue.8, pp.744826-4840, 2006.
DOI : 10.1128/IAI.00081-06

J. Sharma, Y. Zhong, F. Dong, J. Piper, G. Wang et al., Profiling of Human Antibody Responses to Chlamydia trachomatis Urogenital Tract Infection Using Microplates Arrayed with 156 Chlamydial Fusion Proteins, Infection and Immunity, vol.74, issue.3, pp.1490-1499, 2006.
DOI : 10.1128/IAI.74.3.1490-1499.2006

G. Zhong, I. Toth, R. Reid, and R. Brunham, Immunogenicity evaluation of a lipidic amino acid-based synthetic peptide vaccine for Chlamydia trachomatis, J Immunol, vol.151, issue.7, pp.3728-3736, 1993.

F. Dong, Y. Zhong, B. Arulanandam, and G. Zhong, Production of a Proteolytically Active Protein, Chlamydial Protease/Proteasome-Like Activity Factor, by Five Different Chlamydia Species, Infection and Immunity, vol.73, issue.3, pp.1868-1872, 2005.
DOI : 10.1128/IAI.73.3.1868-1872.2005