PDP: protein domain parser, Bioinformatics, vol.19, issue.3, pp.429-430, 2003. ,
DOI : 10.1093/bioinformatics/btg006
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/19/3/429
Data growth and its impact on the SCOP database: new developments, Nucleic Acids Research, vol.36, issue.Database, pp.419-425, 2008. ,
DOI : 10.1093/nar/gkm993
The protein data bank: A computer-based archival file for macromolecular structures, Journal of Molecular Biology, vol.112, issue.3, pp.535-542, 1977. ,
DOI : 10.1016/S0022-2836(77)80200-3
Alternative splicing and protein structure evolution, Nucleic Acids Research, vol.36, issue.2, pp.550-558, 2008. ,
DOI : 10.1093/nar/gkm1054
URL : http://doi.org/10.1093/nar/gkm1054
Comparing Models of Evolution for Ordered and Disordered Proteins, Molecular Biology and Evolution, vol.27, issue.3, pp.609-621, 2010. ,
DOI : 10.1093/molbev/msp277
Assessing Determinants of Exonic Evolutionary Rates in Mammals, Molecular Biology and Evolution, vol.29, issue.10, 2012. ,
DOI : 10.1093/molbev/mss116
Independent Effects of Alternative Splicing and Structural Constraint on the Evolution of Mammalian Coding Exons, Molecular Biology and Evolution, vol.29, issue.1, pp.187-193, 2012. ,
DOI : 10.1093/molbev/msr182
Extending CATH: increasing coverage of the protein structure universe and linking structure with function, Nucleic Acids Research, vol.39, issue.Database, pp.420-426, 2011. ,
DOI : 10.1093/nar/gkq1001
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004. ,
DOI : 10.1093/nar/gkh340
Protein Peeling 3D: new tools for analyzing protein structures, Bioinformatics, vol.27, issue.1, pp.132-133, 2011. ,
DOI : 10.1093/bioinformatics/btq610
URL : https://hal.archives-ouvertes.fr/inserm-00568165
'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments, Bioinformatics, vol.22, issue.2, pp.129-133, 2006. ,
DOI : 10.1093/bioinformatics/bti773
URL : https://hal.archives-ouvertes.fr/inserm-00133725
Protein Peeling 2: a web server to convert protein structures into series of protein units, Nucleic Acids Research, vol.34, issue.Web Server, pp.75-78, 2006. ,
DOI : 10.1093/nar/gkl292
URL : https://hal.archives-ouvertes.fr/inserm-00133731
Partitioning Protein Structures into Domains: Why Is it so Difficult?, Journal of Molecular Biology, vol.361, issue.3, pp.562-590, 2006. ,
DOI : 10.1016/j.jmb.2006.05.060
The FSSP database of structurally aligned protein fold families, Nucleic Acids Res, vol.22, pp.3600-3609, 1994. ,
High-throughput DNA sequencing - concepts and limitations, BioEssays, vol.11, issue.6, pp.524-536, 2010. ,
DOI : 10.1002/bies.200900181
Predicting Functional Alternative Splicing by Measuring RNA Selection Pressure from Multigenome Alignments, PLoS Computational Biology, vol.17, issue.12, p.1000608, 2009. ,
DOI : 10.1371/journal.pcbi.1000608.s009
Handbook of biological statistics, pp.232-237, 2009. ,
RNA-seq: technical variability and sampling, BMC Genomics, vol.18, issue.2, p.293, 2011. ,
DOI : 10.1093/bioinformatics/18.11.1438
Functional Implications of Structural Predictions for Alternative Splice Proteins Expressed in Her2/neu???Induced Breast Cancers, Journal of Proteome Research, vol.10, issue.12, pp.5503-5511, 2011. ,
DOI : 10.1021/pr200772w
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
CATH ??? a hierarchic classification of protein domain structures, Structure, vol.5, issue.8, pp.1093-1108, 1997. ,
DOI : 10.1016/S0969-2126(97)00260-8
Foldons, protein structural modules, and exons., Proceedings of the National Academy of Sciences, vol.93, issue.5, pp.2008-2013, 1996. ,
DOI : 10.1073/pnas.93.5.2008
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC39900
The Natural History of Protein Domains, Annual Review of Biophysics and Biomolecular Structure, vol.31, issue.1, pp.45-71, 2002. ,
DOI : 10.1146/annurev.biophys.31.082901.134314
Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing, Genome Research, vol.19, issue.7, pp.1309-1315, 2009. ,
DOI : 10.1101/gr.089151.108
R: a language and environment for statistical computing, 2012. ,
Letter, Toxicological Sciences, vol.75, issue.1, pp.177-181, 1974. ,
DOI : 10.1093/toxsci/kfg176
Structural and functional diversity generated by alternative mRNA splicing, Trends in Biochemical Sciences, vol.30, issue.9, pp.515-521, 2005. ,
DOI : 10.1016/j.tibs.2005.07.001
Differential expression in RNA-seq: A matter of depth, Genome Research, vol.21, issue.12, pp.2213-2223, 2011. ,
DOI : 10.1101/gr.124321.111
The implications of alternative splicing in the ENCODE protein complement, Proc Natl Acad Sci, vol.104, pp.5495-5500, 2007. ,
DDBASE2.0: updated domain database with improved identification of structural domains, Bioinformatics, vol.19, issue.14, pp.1760-1764, 2003. ,
DOI : 10.1093/bioinformatics/btg233
PISCES: recent improvements to a PDB sequence culling server, Nucleic Acids Research, vol.33, issue.Web Server, pp.94-98, 2005. ,
DOI : 10.1093/nar/gki402
The DISOPRED server for the prediction of protein disorder, Bioinformatics, vol.20, issue.13, pp.2138-2139, 2004. ,
DOI : 10.1093/bioinformatics/bth195
Nucleation, Rapid Folding, and Globular Intrachain Regions in Proteins, Proceedings of the National Academy of Sciences, vol.70, issue.3, pp.697-701, 1973. ,
DOI : 10.1073/pnas.70.3.697
Acquisition of Three-Dimensional Structure of Proteins, Annual Review of Biochemistry, vol.42, issue.1, pp.135-158, 1973. ,
DOI : 10.1146/annurev.bi.42.070173.001031
Computational methods for protein structure prediction and modeling, 2006. ,
PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007. ,
DOI : 10.1093/molbev/msm088
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.322.1650