2.2 years ago by
Cincinnati Children's Hospital Medical Center
If you haven't checked it out already, you can find extensive background information on the algorithms used for alternative splicing detection and interpretation in AltAnalyze here:
Publications using AltAnalyze can be found here:
Also check out Figure 2 in the following paper that describes why you see domain predictions that wouldn't not be directly overlapping with a specific splicing event:
Basically, when comparing two reciprocal junctions with the ASPIRE algorithm, the software is looking for pairs of minimally different RNA-isoforms (exon composition) that contain and don't contain the compared junctions. The associated proteins for those isoforms are then compared along with any protein isoform differences including retained introns. Some retained introns are actually very small (hundreds of nucleotides) and are effectively exons with exon IDs assigned by the AltAnalyze software rather than intron IDs. Such isoforms may include other exons that are different since some splicing events co-occur with others. This may not be the actual case, but rather a novel isoform is produced which only impacts that exons. For that reason protein isoform and domain interaction predictions are speculative. A tool that is distributed with AltAnalyze (AltAnalyze Results Viewer - Grey icon), lets you interactively explore such domain isoform graphs in the context of these spliced junctions and exons.
If concerned about the accuracy of these results, that is a good thing! Splicing results should be considered speculative and followed up with read-level visualization (Sashimi-Plot visualization in AltAnalyze or IGV). Importantly, the legacy splicing algorithms present in the current distributed compiled version of AltAnalyze are not ideal. We have been developing a new algorithm called MultiPath-PSI which is far superior in terms of sensitivity and specificity (see simulation validation and algorithm comparisons):
You can apply this algorithm if use the latest version of the software from GitHub. The results will be stored as described in the above link.
A PyPi python installer is being finalized to install all dependencies on Mac and Windows here, but is still being tested:
pip install --extra-index-url https://testpypi.python.org/pypi AltAnalyze
(type "altanalyze" in a Mac terminal or Windows command prompt to start altanalyze)
Let us know if you need help with any of these analyses (email@example.com).