A. Yaseen and Y. Li, Context-based features enhance protein secondary structure prediction accuracy, J Chem Inf Model, vol.54, pp.992-1002, 2014.

C. Mirabello and P. G. Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility, Bioinformatics, vol.29, pp.2056-2064, 2013.

A. Ghouila, I. Florent, F. Z. Guerfali, and N. Terrapon, Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection, PLoS One, vol.9, p.95275, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01060276

S. Aganezov and M. A. Alekseyev, On pairwise distances and median score of three genomes under DCJ, BMC Bioinformatics, vol.13, p.1, 2012.

D. M. Krylov, Y. I. Wolf, I. B. Rogozin, and E. V. Koonin, Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution, Genome Res, vol.13, pp.2229-2264, 2003.

E. Borenstein, T. Shlomi, E. Ruppin, and R. Sharan, Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes, Nucleic Acids Res, vol.35, p.7, 2007.

T. Song and H. Gu, Discovering short linear protein motif based on selective training of profile hidden Markov models, J Theor Biol, vol.377, pp.75-84, 2015.

M. Kalkatawi, I. Alam, and V. B. Bajic, BEACON: automated tool for bacterial GEnome annotation ComparisON, BMC Genomics, vol.16, p.616, 2015.

A. Nazarian and S. A. Gezan, GenoMatrix: a software package for pedigreebased and genomic prediction analyses on complex traits, J Hered, vol.107, pp.372-381, 2016.

K. Glass and M. Girvan, Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of, Gene Sets. Sci. Rep, vol.4, p.4191, 2014.

M. Lawrence, W. Huber, H. Pagès, and P. Aboyoun, Software for computing and annotating genomic ranges, PLoS Comput Biol, vol.9, p.1003118, 2013.

N. Riddell and S. G. Crewther, Integrated Comparison Of GWAS, transcriptome, and proteomics studies highlights similarities in the biological basis of animal and human MyopiaIntegrated comparison of myopia omics studies, Invest Ophthalmol Vis Sci, vol.58, pp.660-669, 2017.

L. Shen, N. Shao, X. Liu, and I. Maze, diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates, PLoS One, vol.8, p.65598, 2013.

A. R. Quinlan, BEDTools: the Swiss-Army tool for genome feature analysis, Curr Protoc Bioinforma, vol.47, pp.11-12, 2014.

W. W. Daniel, C. L. Cross, and . Biostatistics, A Foundation For analysis in Health Sciences, pp.22-23, 2013.

G. M. Baker and P. K. Trivedi, Estimation of unemployment duration from grouped data: a comparative study, J Labor Econ, vol.3, pp.153-74, 1985.

R. Prytuliak, M. Volkmer, M. Meier, and B. H. Habermann, HH-MOTiF: de novo detection of short linear motifs in proteins by hidden Markov model comparisons, Nucleic Acids Res, vol.45, pp.470-477, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01692042

M. Do?ruel, T. A. Down, and T. J. Hubbard, NestedMICA as an ab initio protein motif discovery tool, BMC Bioinformatics, vol.9, p.19, 2008.

H. Dinkel, K. Van-roey, S. Michael, and M. Kumar, ELM 2016-data update and new functionality of the eukaryotic linear motif resource, Nucleic Acids Res, vol.44, pp.294-300, 2016.

M. Falb, F. Pfeiffer, P. Palm, and K. Rodewald, Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis

, Genome Res, vol.15, pp.1336-1379, 2005.

F. Pfeiffer and D. Oesterhelt, A manual curation strategy to improve genome annotation: application to a set of Haloarchael genomes, Life, vol.5, pp.1427-1471, 2015.

K. Clark, I. Karsch-mizrachi, D. J. Lipman, and J. Ostell, Nucleic Acids Res, vol.44, pp.67-72, 2016.

N. A. O'leary, M. W. Wright, J. R. Brister, and S. Ciufo, Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation, Nucleic Acids Res, vol.44, pp.733-778, 2016.

N. Coordinators, Database resources of the National Center for biotechnology information, Nucleic Acids Res, vol.42, pp.7-17, 2014.

G. Santos, A. J. Schroeder, J. L. Goodman, and V. B. Strelets, FlyBase: introduction of the Drosophila Melanogaster release 6 reference genome assembly and large-scale migration of genome annotations, Nucleic Acids Res, vol.43, pp.690-697, 2015.

B. Nunes, I. Natário, and M. L. Carvalho, Time series methods for obtaining excess mortality attributable to influenza epidemics, Stat Methods Med Res, vol.20, pp.331-376, 2011.

M. B. Nielsen, M. S. Birkeland, M. B. Hansen, and S. Knardahl, Victimization from workplace bullying after a traumatic event: time-lagged relationships with symptoms of posttraumatic stress, Int Arch Occup Environ Health, vol.90, pp.411-432, 2017.

. The-uniprot-consortium, UniProt: the universal protein knowledgebase, Nucleic Acids Res, vol.45, pp.158-69, 2017.

R. J. Edwards, N. E. Davey, and D. C. Shields, SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins, PLoS One, vol.2, p.967, 2007.

T. L. Bailey, N. Williams, C. Misleh, and W. W. Li, MEME: discovering and analyzing DNA and protein sequence motifs, Nucleic Acids Res, vol.34, pp.369-73, 2006.