SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation

• Published in: BMC bioinformatics Vol. 20; no. 1; pp. 231 - 7
• Main Authors: Ungerleider, Nathan, Flemington, Erik
• Format: Journal Article
• Language: English
• Published: London BioMed Central 08.05.2019; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Alternative splicing; Alternative Splicing - genetics; Binding sites; Bioinformatics; Biomedical and Life Sciences; Biosynthesis; circRNA; Circular RNA; Circularity; Complexity; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Data visualization; Displays (Marketing); Downloading; Eukaryotes; Exon skipping; Exons - genetics; Gene expression; Gene sequencing; Genes; Genetic research; High-Throughput Nucleotide Sequencing; Humans; Intron retention; Isoform; Isoforms; Life Sciences; Methods; Microarrays; Next-generation sequencing; Protein binding; Proteins; Ribonucleic acid; RNA; RNA - genetics; RNA - metabolism; RNA sequencing; RNA splicing; RNA Splicing - genetics; RNA, Circular; RNA-binding protein; RNA-Binding Proteins - metabolism; Science; Scientific software; Software; Source code; Splicing; Transcription; Visualization; United States; Alternative splicing; Isoform; Intron retention; circRNA; Exon skipping
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-019-2865-7

Background In eukaryotes, most genes code for multiple transcript isoforms that are generated through the complex and tightly regulated process of RNA splicing. Despite arising from identical precursor transcripts, alternatively spliced RNAs can have dramatically different functions. Transcriptome complexity is elevated further by the production of circular RNAs (circRNAs), another class of mature RNA that results from the splicing of a downstream splice donor to an upstream splice acceptor. While there has been a rapid expansion of circRNA catalogs in the last few years through the utilization of next generation sequencing approaches, our understanding of the mechanisms and regulation of circular RNA biogenesis, the impact that circRNA generation has on parental transcript processing, and the functions carried out by circular RNAs remains limited. Results Here, we present a visualization and analysis tool, SpliceV, that rapidly plots all relevant forward- and back-splice data, with exon and single nucleotide level coverage information from RNA-seq experiments in a publication quality format. SpliceV also integrates analysis features that assist investigations into splicing regulation and transcript functions through the display of predicted RNA binding protein sites and the configuration of repetitive elements along the primary transcript. Conclusions SpliceV is an easy-to-use splicing visualization tool, compatible with both Python 2.7 and 3+, and distributed under the GNU Public License. The source code is freely available for download at https://github.com/flemingtonlab/SpliceV and can be installed from PyPI using pip.