tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing

• Published in: Genome Biology Vol. 21; no. 1; p. 119
• Main Authors: de la Fuente, Lorena, Arzalluz-Luque, Ángeles, Tardáguila, Manuel, del Risco, Héctor, Martí, Cristina, Tarazona, Sonia, Salguero, Pedro, Scott, Raymond, Lerma, Alberto, Alastrue-Agudo, Ana, Bonilla, Pablo, Newman, Jeremy R. B., Kosugi, Shunichi, McIntyre, Lauren M., Moreno-Manzano, Victoria, Conesa, Ana
• Format: Journal Article
• Language: English
• Published: London BioMed Central 18.05.2020; Springer Nature B.V; BMC
• Subjects: algorithms; Alternative Splicing; Animal Genetics and Genomics; Animals; Annotations; Bioinformatics; Biology; Biomedical and Life Sciences; Computer applications; computer software; Evolutionary Biology; Gene expression; Gene Expression Profiling - methods; Gene regulation; Human Genetics; Java; Life Sciences; messenger RNA; Mice; Microbial Genetics and Genomics; Oligodendrocyte Precursor Cells - metabolism; Plant Genetics and Genomics; Polyadenylation; Post-transcription; Protein Isoforms - metabolism; Proteins; Researchers; Ribonucleic acid; RNA; sequence analysis; Software; Splicing; Studies; Transcriptomics; User interface
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-020-02028-w

Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isoform-centered functional analysis. Here, we present tappAS, the first framework to enable a comprehensive Functional Iso-Transcriptomics (FIT) analysis, which is effective at revealing the functional impact of context-specific post-transcriptional regulation. tappAS uses isoform-resolved annotation of coding and non-coding functional domains, motifs, and sites, in combination with novel analysis methods to interrogate different aspects of the functional readout of transcript variants and isoform regulation. tappAS software and documentation are available at https://app.tappas.org .