down-stream) was used as input when possible; if not, the requested size of the constitutive splice site was used for the corresponding software NA: not available. The complete list of references for each bioinformatics resource is available in Supp Using geneid to identify genes, Curr Protoc Bioinformatics Chapter, vol.4, issue.3, 2007. ,
Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA, Nucleic Acids Research, vol.26, issue.20, pp.4748-57, 1998. ,
DOI : 10.1093/nar/26.20.4748
Prediction of human mRNA donor and acceptor sites from the DNA sequence, Journal of Molecular Biology, vol.220, issue.1, pp.49-65, 1991. ,
DOI : 10.1016/0022-2836(91)90380-O
Prediction of complete gene structures in human genomic DNA, Journal of Molecular Biology, vol.268, issue.1, pp.78-94, 1997. ,
DOI : 10.1006/jmbi.1997.0951
ESEfinder: a web resource to identify exonic splicing enhancers, Nucleic Acids Research, vol.31, issue.13, pp.3568-71, 2003. ,
DOI : 10.1093/nar/gkg616
Human Splicing Finder: an online bioinformatics tool to predict splicing signals, Nucleic Acids Research, vol.37, issue.9, p.67, 2009. ,
DOI : 10.1093/nar/gkp215
URL : https://hal.archives-ouvertes.fr/inserm-00396239
SplicePort--An interactive splice-site analysis tool, Nucleic Acids Research, vol.35, issue.Web Server, pp.285-91, 2007. ,
DOI : 10.1093/nar/gkm407
Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation, Human Molecular Genetics, vol.14, issue.11, pp.1559-68, 2005. ,
DOI : 10.1093/hmg/ddi164
Missense, Nonsense, and Neutral Mutations Define Juxtaposed Regulatory Elements of Splicing in Cystic Fibrosis Transmembrane Regulator Exon 9, Journal of Biological Chemistry, vol.278, issue.29, pp.26580-26588, 2003. ,
DOI : 10.1074/jbc.M212813200
New type of disease causing mutations: the example of the composite exonic regulatory elements of splicing in CFTR exon 12, Human Molecular Genetics, vol.12, issue.10, pp.1111-1131, 2003. ,
DOI : 10.1093/hmg/ddg131
Prediction of single-nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6, Human Mutation, vol.35, issue.4, pp.436-480, 2011. ,
DOI : 10.1002/humu.21458
URL : https://hal.archives-ouvertes.fr/hal-00620579
Improved Splice Site Detection in Genie, Journal of Computational Biology, vol.4, issue.3, pp.311-334, 1997. ,
DOI : 10.1089/cmb.1997.4.311
SROOGLE: webserver for integrative, user-friendly visualization of splicing signals, Nucleic Acids Research, vol.37, issue.Web Server, pp.189-92, 2009. ,
DOI : 10.1093/nar/gkp320
Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes, Genome Research, vol.18, issue.1, pp.88-103, 2008. ,
DOI : 10.1101/gr.6818908
Genomic features defining exonic variants that modulate splicing, Genome Biology, vol.11, issue.2, p.20, 2010. ,
DOI : 10.1186/gb-2010-11-2-r20
URL : http://doi.org/10.1186/gb-2010-11-2-r20
Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals, Journal of Computational Biology, vol.11, issue.2-3, pp.377-94, 2004. ,
DOI : 10.1089/1066527041410418