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The next generation sequencing (NGS) technologies, producing thousands and millions of sequences in one run and at lower cost, have been applied to many biological research fields. RNA-Seq is the application of NGS to the mRNA transcriptome research. 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.

Highlights of SplicingViewer:

  • Provide pipeline to detect splice junctions and annotate the alternative splicing patterns, given known gene model.

  • Employ the SAM/BAM format, which can be generated natively by many mapping tools or can be convert from the mapping results in other formats, as the input data format.

  • Provide a user-friendly interface to display alternative splicing patterns and large-scale RNA-Seq short reads mapping result in memory efficient and quick manner.

  • Flexible customizable configure supports zooming, font and colors definition schemes.

  • Introduce the workspace where users can easily create new session, save the intermediate result.

A typical screenshot of SplicingViewer:

Copyright©2010, Institute of Genomic Medicine/Zhejiang Provincial Key Laboratory of Medical Genetics,
Wenzhou Medical College, Wenzhou 325035, China.