How to find out the domains encoded by each exon and predict gene isoform role/function?

Question

[danson.wooi]

I have a list of differentially expressed isoforms that I would like to analyse the sequence of. Basically if an isoform skips an exon I want to know what the consequences of skipping that exon is. Are there any tools that can help me with this? Such as something that might determine where protein domains are based on sequence? Is there a way to do this for multiple transcript sequences (i.e a pipeline I can use?)?

Answer 1

[caggtaagtat]

We just started to test the R package IsoformswitchanalyseR, which could be interesting for you. It is very well documented and gives you exactly this information. You can use it with e.g. salmon count matrices