A. Andreeva, A. Prlic, T. Hubbard, and A. G. Murzin, SISYPHUS--structural alignments for proteins with non-trivial relationships, Nucleic Acids Research, vol.35, issue.Database, pp.253-259, 2007.
DOI : 10.1093/nar/gkl746

S. Aubourg, N. Boudet, M. Kreis, and A. Lecharny, In Arabidopsis thaliana, 1% of the genome codes for a novel protein family unique to plants, Plant Molecular Biology, vol.42, issue.4, pp.603-613, 2000.
DOI : 10.1023/A:1006352315928

A. Bateman, L. Coin, R. Durbin, R. D. Finn, V. Hollich et al., The PFAM protein families database, Nuc Acids Res, issue.S1, pp.32-138, 2004.
URL : https://hal.archives-ouvertes.fr/hal-01294685

E. Bornberg-bauer, F. Beaussart, S. K. Kummerfeld, S. A. Teichmann, and J. Weiner, The evolution of domain arrangements in proteins and interaction networks, CMLS Cellular and Molecular Life Sciences, vol.62, issue.4, pp.435-445, 2005.
DOI : 10.1007/s00018-004-4416-1

L. Coin, A. Bateman, and R. Durbin, Enhanced protein domain discovery by using language modeling techniques from speech recognition, Proceedings of the National Academy of Sciences, vol.100, issue.8, pp.4516-4520, 2003.
DOI : 10.1073/pnas.0737502100

S. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-763, 1998.
DOI : 10.1093/bioinformatics/14.9.755

E. Kotera, M. Tasaka, and T. Shikanai, A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts, Nature, vol.101, issue.7023, pp.326-356, 2005.
DOI : 10.1073/pnas.96.26.15324

A. Krogh, An introduction to hidden Markov models for biological sequences, Computational Methods in Molecular Biology, 1998.
DOI : 10.1016/S0167-7306(08)60461-5

C. Lurin, C. Andres, and S. Aubourg, Genome-Wide Analysis of Arabidopsis Pentatricopeptide Repeat Proteins Reveals Their Essential Role in Organelle Biogenesis, THE PLANT CELL ONLINE, vol.16, issue.8, pp.2089-2103, 2004.
DOI : 10.1105/tpc.104.022236

R. Munford, P. Sheppard, and . Hara, Saposin-like proteins (SAPLIP) carry out diverse functions on a common backbone structure, J. Lipid Res, vol.36, issue.8, pp.1653-1663, 1995.

A. G. Murzin, S. Brenner, T. Hubbard, and C. Chothia, SCOP: A structural classification of proteins database for the investigation of sequences and structures, Journal of Molecular Biology, vol.247, issue.4, pp.536-540, 1995.
DOI : 10.1016/S0022-2836(05)80134-2

L. R. Rabiner, A tutorial on hidden Markov models and selected applications in speech recognition, Proc. IEEE, pp.257-286, 1989.

S. Uliel, A. Fliess, A. Amir, and R. Unger, A simple algorithm for detecting circular permutations in proteins, Bioinformatics, vol.15, issue.11, pp.930-936, 1999.
DOI : 10.1093/bioinformatics/15.11.930

S. Uliel, A. Fliess, and R. Unger, Naturally occurring circular permutations in proteins, Protein Engineering Design and Selection, vol.14, issue.8, pp.533-542, 2001.
DOI : 10.1093/protein/14.8.533

J. Weiner, T. Geraint, and E. Bornberg-bauer, Rapid motif-based prediction of circular permutations in multi-domain proteins, Bioinformatics, vol.21, issue.7, pp.932-937, 2005.
DOI : 10.1093/bioinformatics/bti085