M. Garber, M. Grabherr, M. Guttman, and C. Trapnell, Computational methods for transcriptome annotation and quantification using RNA-seq, Nature Methods, vol.19, issue.6, pp.469-77, 2011.
DOI : 10.1093/nar/gkq1015

T. Steijger, J. Abril, P. Engstrom, F. Kokocinski, T. Hubbard et al., Assessment of transcript reconstruction methods for RNA-seq, Nature Methods, vol.330, issue.12, pp.1177-84, 2013.
DOI : 10.1093/bioinformatics/bts635

URL : https://hal.archives-ouvertes.fr/hal-00909081

C. Angelini, D. Canditiis, D. , D. Feis, and I. , Computational approaches for isoform detection and estimation: good and bad news, BMC Bioinformatics, vol.15, issue.1, pp.1-25, 2014.
DOI : 10.1186/1471-2105-15-135

J. Jänes, F. Hu, A. Lewin, and E. Turro, A comparative study of RNA-seq analysis strategies, Briefings in Bioinformatics, vol.16, issue.6, pp.932-972, 2015.
DOI : 10.1093/bib/bbv007

K. Hayer, A. Pizarro, N. Lahens, J. Hogenesch, and G. Grant, Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from rna-seq data, Bioinformatics, issue.24, pp.313938-313983, 2015.

M. Pertea, G. Pertea, C. Antonescu, T. Chang, J. Mendell et al., StringTie enables improved reconstruction of a transcriptome from RNA-seq reads, Nature Biotechnology, vol.16, issue.3, pp.290-295, 2015.
DOI : 10.1038/nbt.3122

O. Kelemen, P. Convertini, Z. Zhang, Y. Wen, M. Shen et al., Function of alternative splicing, Gene, vol.514, issue.1, pp.1-30, 2013.
DOI : 10.1016/j.gene.2012.07.083

I. Korf, P. Flicek, D. Duan, and M. Brent, Integrating genomic homology into gene structure prediction, Bioinformatics, vol.17, issue.Suppl 1, pp.140-148, 2001.
DOI : 10.1093/bioinformatics/17.suppl_1.S140

J. Fong, T. Murphy, and K. Pruitt, Comparison of RefSeq protein-coding regions in human and vertebrate genomes, BMC Genomics, vol.14, issue.1, p.1, 2013.
DOI : 10.1093/bioinformatics/btm076

A. Souvorov, Y. Kapustin, B. Kiryutin, V. Chetvernin, T. Tatusova et al., Gnomon ? ncbi eukaryotic gene prediction tool, National Center for Biotechnology Information, Bethesda, 2010.

F. Zambelli, G. Pavesi, C. Gissi, D. Horner, and G. Pesole, Assessment of orthologous splicing isoforms in human and mouse orthologous genes, BMC Genomics, vol.11, issue.1, p.534, 2010.
DOI : 10.1186/1471-2164-11-534

M. Hiller, K. Huse, K. Szafranski, N. Jahn, J. Hampe et al., Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity, Nature Genetics, vol.321, issue.12, pp.1255-57, 2004.
DOI : 10.1101/gr.1017303

T. Thanaraj and F. Clark, Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions, Nucleic Acids Research, vol.29, issue.12, pp.2581-93, 2001.
DOI : 10.1093/nar/29.12.2581

A. Ouangraoua, K. Swenson, and A. Bergeron, On the Comparison of Sets of Alternative Transcripts, Bioinformatics Research and Applications, vol.7292, pp.201-213, 2012.
DOI : 10.1007/978-3-642-30191-9_19

URL : https://hal.archives-ouvertes.fr/hal-00750031

P. Sellers, The theory and computation of evolutionary distances: Pattern recognition, Journal of Algorithms, vol.1, issue.4, pp.359-73, 1980.
DOI : 10.1016/0196-6774(80)90016-4

A. Yates, W. Akanni, M. Amode, D. Barrell, K. Billis et al., Ensembl 2016, Nucleic Acids Research, vol.44, issue.D1, pp.710-716, 2016.
DOI : 10.1093/nar/gkv1157

M. Burset and R. Guigo, Evaluation of Gene Structure Prediction Programs, Genomics, vol.34, issue.3, pp.353-67, 1996.
DOI : 10.1006/geno.1996.0298

C. Farrell, O. Leary, N. Harte, R. Loveland, J. Wilming et al., Current status and new features of the Consensus Coding Sequence database, Nucleic Acids Research, vol.42, issue.D1, pp.865-872, 2014.
DOI : 10.1093/nar/gkt1059