title: Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico.
abstract: Next-generation sequencing techniques have been rapidly emerging. However, the massive sequencing reads hide a great deal of unknown important information. Advances have enabled researchers to discover alternative splicing (AS) sites and isoforms using computational approaches instead of molecular experiments. Given the importance of AS for gene expression and protein diversity in eukaryotes, detecting alternative splicing and isoforms represents a hot topic in systems biology and epigenetics research. The computational methods applied to AS prediction have improved since the emergence of next-generation sequencing. In this study, we introduce state-of-the-art research on AS and then compare the research methods and software tools available for AS based on next-generation sequencing reads. Finally, we discuss the prospects of computational methods related to AS.
authors.affiliation: Department of Infectious Diseases, The Affiliated Chenggong Hospital of Xiamen University, The 174th Hospital of the Chinese People's Liberation Army, Xiamen, Fujian 361000, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Min
authors.affiliation: Department of Infectious Diseases, The Affiliated Chenggong Hospital of Xiamen University, The 174th Hospital of the Chinese People's Liberation Army, Xiamen, Fujian 361000, China.
authors.forename: Sumei
authors.initials: S
authors.lastname: Wang
authors.affiliation: Department of Infectious Diseases, The Affiliated Chenggong Hospital of Xiamen University, The 174th Hospital of the Chinese People's Liberation Army, Xiamen, Fujian 361000, China.
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D003198:Computer Simulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D022821:RNA Splice Sites / Q000235:genetics; D011795:Surveys and Questionnaires
chemical_list: D020033:Protein Isoforms; D022821:RNA Splice Sites