SplicingViewer
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Application data |
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| Created by | Qi Liu, Linglin Zhou, Huabin Hou, Erle Zhu, Enjian Shen, Fangqing Zhao, Jinyu Wu, Zhongsheng Sun |
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| Biological application domain(s) | RNA-Seq, Genomics |
| Principal bioinformatics method(s) | Mapping |
| Technology | Illumina |
| Created at | Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou，China |
| Maintained? | Yes |
| Input format(s) | SAM/BAM |
| Output format(s) | GFF, Tab |
| Software features | GUI, command line, Data Visualisation |
| Programming language(s) | Java |
| Licence | GPL, Commercial, BioLicense, LGPL, BioLicense, BSD License |
| Operating system(s) | Linux, Windows, Mac OS X |
Summary: SplicingViewer is an integrated tool developed to enable users to detect the splice junctions, annotate alternative splicing events, and visualization of the patterns of alternative splicing events.
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Description
RNA-Seq can not only provide more efficient and precise way to measure the content of gene expression, but also can be used to detect other post-transcription events, such as alternative splicing. Alternative splicing is key RNA splicing process by which one gene can generate multiple protein isoforms. So the limited number of genes in an organism can form large complex proteome by alternative splicing. There are mainly seven types of alternative splicing exist, which are skipped exons (SE), mutually exclusive exons (MXE), alternative 5' splice sites (A5SS), alternative 3' splice sites (A3SS), alternative first exons (AFE), alternative last exons (ALE), and retained intron (RI). Here we developed an integrated tool-SplicingViewer, which can detect the splice junctions based on known gene models, annotate the alternative splicing patterns based on the splice junctions, and visualize the patterns of alternative splicing events. In addition, as a viewer, SplicingViewer can also be used to display the RNA-Seq reads mapping results with high speed and lower memory spend.
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