Department of Bioinformatics and Computational Biology

Home > Public Software > SpliceSeq > GUI


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DescriptionA tool for investigating alternative mRNA splicing in next generation mRNA sequence data
Development Information
Current version2.1
PlatformsPlatform independent
LicenseFreely available for academic and commercial use
Last updatedFebruary 21, 2014
Citation Ryan, M. C., Cleland, J., Kim, R.G., Wong, W. C., Weinstein, J. N., SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts, Bioinformatics 28 (18) p.2385 (2012). 
Help and Support

Graphical User Interface Overview

The graphical user interface of SpliceSeq can be divided into 3 areas.

Data Selection Bar

Data Selection Bar is where the data is loaded, the View type and Dataset are chosen, as well as where the program configurations are set, and consists of the Menu, View Combobox, DataSet Combobox and Gene Finder.

Menu contains the miscellaneous items that are functionally distinct from the other parts of the interface, and consists of 3 root level items:

View Combobox allows one to choose from five different view modes depending on the type of analysis you wish to explore:

DataSet Combobox is populated with relevant datasets upon selecting a view mode. Choosing an item here will populate the Results Panel with the list of detected Splice Events for the selected dataset. SpliceSeq data is organized by study so you will need to click on the appropriate study folder to see the samples / groups / comparisons in the study.

Gene Finder allows one to jump to a gene of interest in the Results Panel. Its auto-complete function will suggest possible matches when you type at least 2 letters in the text box. Clicking the arrow next to the gene symbol will go to the next occurrence of the symbol in the list. (Genes may have multiple splice events)

Results Panel

Results Panel is where the list of Splice Events for the selected sample or group are displayed.

There are 3 tabs to choose from:

Detail Panel

Detail Panel is populated with the respective splice graph and protein expression information upon choosing an item in the Results Panel. There are three tabs in the Detail Panel.

Graph Image Tab

Graph Image Tab displays the splice graph of the gene with exons as boxes and arcing lines as splices.

Navigating the splice graph is done using the mouse.

Protein Sequence Tab

Protein Sequence Tab provides information on predicted protein isoforms based on splice graph expression, and consists of three distinct sections.

Detailed explanation of the tab is shown below.

To get a fuller description of the UniProt feature codes, select the Feature Legend/Filter… button in the upper left of Protein Sequence Tab. This displays a pop-up window with the feature codes. The checkboxes in the legend may also be used to selectively turn on / off the display of various types of features. Also, Protein Sequence Tab’s image can be zoomed in and out by clicking Zoom in/Zoom out button right to Feature Legend/Filter… button. Saving the image of Protein Sequence Tab is possible by clicking Save Image… button.

Exon Info Tab

Exon Info Tab lists detailed information about each exon in the gene’s splice graph.