K. Haldar, S. Kamoun, N. L. Hiller, S. Bhattacharje, and C. Ooij, Common infection strategies of pathogenic eukaryotes, Nature Reviews Microbiology, vol.440, issue.12, pp.922-931, 2006.
DOI : 10.1038/nrmicro1549

J. P. Kreier, Infection, resistance and immunity, 2002.

H. Ochman and N. A. Moran, Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis, Science, vol.292, issue.5519, pp.1096-1099, 2001.
DOI : 10.1126/science.1058543

J. Richardson, The Anatomy and Taxonomy of Protein Structure, Adv Protein Chem, vol.34, pp.167-339, 1981.
DOI : 10.1016/S0065-3233(08)60520-3

H. Hegyi and M. Gerstein, Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins, Genome Research, vol.11, issue.10, pp.1632-1640, 2001.
DOI : 10.1101/gr. 183801

R. Finn, The Pfam protein families database, Nucleic Acids Research, vol.36, issue.Database, pp.281-288, 2008.
DOI : 10.1093/nar/gkm960
URL : https://hal.archives-ouvertes.fr/hal-01294685

R. Durbin, Biological sequence analysis: probabilistic models of proteins and nucleic acids, 1998.
DOI : 10.1017/CBO9780511790492

P. Ward1, L. Equinet, J. Packer, and C. Doerig, Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote, BMC Genomics, vol.5, issue.1, p.79, 2004.
DOI : 10.1186/1471-2164-5-79

N. Terrapon, O. Gascuel, É. Maréchal, and L. Bréhélin, Detection of new protein domains using co-occurrence: application to Plasmodium falciparum, Bioinformatics, vol.25, issue.23, pp.253077-3083, 2009.
DOI : 10.1093/bioinformatics/btp560
URL : https://hal.archives-ouvertes.fr/lirmm-00431171

G. Apic, Domain combinations in archaeal, eubacterial and eukaryotic proteomes, Journal of Molecular Biology, vol.310, issue.2, pp.311-325, 2001.
DOI : 10.1006/jmbi.2001.4776

C. Aurrecoechea, EuPathDB: a portal to eukaryotic pathogen databases, Database issue, pp.415-419, 2010.
DOI : 10.1093/nar/gkp941

C. S. Peacock, Comparative genomic analysis of three Leishmania species that cause diverse human disease, Nature Genetics, vol.13, issue.7, pp.839-847, 2007.
DOI : 10.1093/bioinformatics/bti1018
URL : https://hal.archives-ouvertes.fr/hal-00169316

G. Synteny and M. , Indels and Synteny Breakpoints as Foci for Species-Specific Genes, PLoS Pathog vol, vol.1, issue.4, pp.349-361, 2005.

J. Blader and J. P. , and its host: impact on parasite growth, development, immune evasion, and virulence, APMIS, vol.117, issue.5-6, pp.458-476, 2009.
DOI : 10.1111/j.1600-0463.2009.02453.x

W. Gatei, C. Wamae, and C. Mbae, Cryptosporidiosis: prevalence, genotype analysis, and symptoms associated with infections in children in Kenya, Am. J. Trop. Med. Hyg, vol.75, issue.1, pp.78-82, 2006.

M. Abrahamsen and T. Templeton, Complete Genome Sequence of the Apicomplexan, Cryptosporidium parvum, Science, vol.304, issue.5669, pp.441-446, 2004.
DOI : 10.1126/science.1094786

J. Tovar, G. León-avila, and L. Sánchez, Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation, Nature, vol.426, issue.6963, pp.172-178, 2003.
DOI : 10.1038/nature01945

H. Morrison, A. Mcarthur, and F. Gillin, Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia, Science, vol.317, issue.5846, pp.1921-1927, 2007.
DOI : 10.1126/science.1143837

F. Beaussart, J. Weiner, and E. Bornberg-bauer, Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN), Bioinformatics, vol.23, issue.14, pp.1834-1836, 2007.
DOI : 10.1093/bioinformatics/btm240

N. Mulder, New developments in the InterPro database, Nucleic Acids Research, vol.35, issue.Database, pp.224-232, 2007.
DOI : 10.1093/nar/gkl841
URL : https://hal.archives-ouvertes.fr/hal-00434830

S. R. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-63, 1998.
DOI : 10.1093/bioinformatics/14.9.755

K. Forslund and E. L. Sonnhammer, Predicting protein function from domain content, Bioinformatics, vol.24, issue.15, pp.1681-1687, 2008.
DOI : 10.1093/bioinformatics/btn312

T. Beißbarth and T. P. Speed, GOstat: find statistically overrepresented Gene Ontologies within a group of genes, Bioinformatics, vol.20, issue.9, pp.1464-1465, 2004.
DOI : 10.1093/bioinformatics/bth088

K. Essien and C. J. Stoeckert, Conservation and divergence of known apicomplexan transcriptional regulons, BMC Genomics, vol.11, issue.1, 2010.
DOI : 10.1186/1471-2164-11-147

E. Bischoff and C. Vaquero, In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum, BMC Genomics, vol.11, issue.1, 2010.
DOI : 10.1186/1471-2164-11-34
URL : https://hal.archives-ouvertes.fr/pasteur-00663529

S. Haile and B. Papadopoulou, Developmental regulation of gene expression in trypanosomatid parasitic protozoa, Current Opinion in Microbiology, vol.10, issue.6, pp.569-77, 2007.
DOI : 10.1016/j.mib.2007.10.001

C. Clayton and M. Shapira, Post-transcriptional regulation of gene expression in trypanosomes and leishmanias, Molecular and Biochemical Parasitology, vol.156, issue.2, pp.93-101, 2007.
DOI : 10.1016/j.molbiopara.2007.07.007

L. A. Hanakahi, H. Sun, and N. J. , High Affinity Interactions of Nucleolin with G-G-paired rDNA, Journal of Biological Chemistry, vol.274, issue.22
DOI : 10.1074/jbc.274.22.15908

G. N. Parkinson, M. P. Lee, and S. Neidle, Crystal structure of parallel quadruplexes from human telomeric DNA, Nature, vol.5, issue.6891, pp.417-876, 2002.
DOI : 10.1038/nature755

N. Maizels, Dynamic roles for G4 DNA in the biology of eukaryotic cells, Nature Structural & Molecular Biology, vol.122, issue.12, pp.1055-1059, 2006.
DOI : 10.1038/nsmb1171

Z. Du, Y. Zhao, and N. Li, Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription, Genome Research, vol.18, issue.2, pp.233-241, 2008.
DOI : 10.1101/gr.6905408

K. Struhl, Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins, Trends in Biochemical Sciences, vol.14, issue.4, pp.137-177, 1989.
DOI : 10.1016/0968-0004(89)90145-X

K. Mathee and G. Narasimhan, Detection of DNA-Binding Helix-Turn-Helix Motifs in Proteins Using the Pattern Dictionary Method, Methods in Enzymology, vol.370, pp.250-264, 2003.
DOI : 10.1016/S0076-6879(03)70022-6

G. Krauss, Biochemistry of Signal transduction and regulation. Second Edition, Chapter 12. Other Receptor Classes, pp.377-384, 2001.

G. M. Pao and M. H. Saier, Response regulators of bacterial signal transduction systems: Selective domain shuffling during evolution, Journal of Molecular Evolution, vol.213, issue.2, pp.136-54, 1995.
DOI : 10.1007/BF00167109

J. Skerker, M. Prasol, B. Perchuk, G. Ee, M. T. Biondi et al., Two-Component Signal Transduction Pathways Regulating Growth and Cell Cycle Progression in a Bacterium: A System-Level Analysis, PLoS Biology, vol.132, issue.10, pp.3-334, 2005.
DOI : 10.1371/journal.pbio.0030334.st003

D. E. Whitworth and P. Cock, Evolution of prokaryotic two-component systems: insights from comparative genomics, Amino Acids, vol.5, issue.3, pp.459-66, 2009.
DOI : 10.1007/s00726-009-0259-2

K. Hybiske and R. Stephens, Exit strategies of intracellular pathogens, Nature Reviews Microbiology, vol.71, issue.2, pp.99-110, 2008.
DOI : 10.1038/nrmicro1821

F. Dragon, A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis, Nature, vol.180, issue.6892, pp.967-970
DOI : 10.1073/PNAS.97.24.13027

K. Bernstein, The small-subunit processome is a ribosome assembly intermediate. Eukaryot Cell, pp.1619-1645, 2004.

M. Albrecht and T. Lengauer, Survey on the PABC recognition motif PAM2, Biochemical and Biophysical Research Communications, vol.316, issue.1, pp.129-167, 2004.
DOI : 10.1016/j.bbrc.2004.02.024

. Nonhoff, Ataxin-2 Interacts with the DEAD/H-Box RNA Helicase DDX6 and Interferes with P-Bodies and Stress Granules, Molecular Biology of the Cell, vol.18, issue.4, pp.1385-1396, 2007.
DOI : 10.1091/mbc.E06-12-1120

M. H. Lamers, H. H. Winterwerp, and T. K. Sixma, The alternating ATPase domains of MutS control DNA mismatch repair, The EMBO Journal, vol.22, issue.3, pp.746-56, 2003.
DOI : 10.1093/emboj/cdg064

P. J. Coronin, Diversity of WD-repeat proteins, Subcell Biochem AND Smith TF. Subcell Biochem, vol.4848, pp.116-2320, 2008.

B. S. Cummings, J. Mchowat, and R. G. Schnellmann, Phospholipase A2s in cell injury and death, J. Pharmacol. Exp. Ther, vol.294, pp.793-799, 2000.