Alternative splicing is commonly thought to be one of the major sources for functional diversity in the proteomes of higher organisms. Only recently, next generation sequencing technologies have become available which allow for sequencing complete tran-scriptomes at very high speed and sequence coverage.
The SpliCQ-score allows for a detailed overview on the (differential) expression of known splice variants present or absent in a set of short reads sequenced in next generation sequencing experiments. Furthermore, it helps to propose and score novel, yet unknown splice variants.
The basic principle how the SpliCQ-score determines the fit of the observations (i.e. reads) to the expectations (i.e. known and novel transcript models) is shown in the Figure below.
Download
You can download the SpliCQ software for detecting (differential) alternative splicing events in next generation sequencing data here.
The software is fully implemented in Java (version 1.5 or higher) and does not require any other libraries than an appropriate Java runtime environment for your system (which can be downloaded from http://java.sun.com).
A short manual is provided within the README File contained in the zip file. Example files to run the program for testing purposes are also available (see README on how to run the examples).
If you have any questions just contact me at fabian dot birzele at boehringer minus ingelheim dot com.
Have fun!