Introduction

SGM (Splicing Graph Modules) is a collection of Python modules housed within a Python package to draw splicing graphs (a form of visual representation of several transcript sequences which may exhibit alternative splicing). An example of the splicing graph that is drawn by SGM (which includes schematic representation of the transcripts that make up the splicing graph) is shown below.

The use of splicing graphs as a visualization tool allows users to quickly and easily make sense of the alternative splicing. Traditional approach represents the transcripts schematically in a multiple sequence alignment like layout (much like the lower half of the example above). This traditional approach requires much effort on the users to make sense of the alternative splicing taking place. In the event where there are large numbers of transcripts, this is nearly impossible.

The Python package allows users to produce splicing graph representation of their data. The package consist of several object oriented classes which users can override or specialize to produce custom splicing graphs.

For users who do not want to bother with any programming, a Python script within the package is available that allows images of splicing graphs to be generated using a series of transcript information as input.

A web service is also available for users to generate images of splicing graphs. This is especially useful for users who do not want to install the package.

The images generated can either be raster (PNG format) or vector (PDF). The vector format is especially useful as it can be scaled to any size and is easily editable using a vector graphics program like Adobe Illustrator.

Contacts

Prof. Shoba Ranganathan
Prof. Tan Tin Wee
Lee Teck Kwong Bernett