Run ProtAnnot Plug-In on UCSC-isoforms in IGB (interactive genome viewer)

Question

[K91]

Dear all,

due to my bachelor thesis, I'm using IGB for my domain-analysis. Unfortunately I'm stuck, and I couldn't find any valuable solutions on the internet. I really hope you can help me.

My problem:

Picture: [SGIP1 isoforms]

Looking at gene SGIP1 in Human, the "RefGene +/-" shows only one isoform, whereas "knownGene" shows multiple one (the ones I'm interested in). Unfortunately I can't run ProtAnnot on those, as I'm getting the Error "You have not selected any gene models.". I can run ProtAnnot on the one of RefGene, but I need the domain informations on all isoforms.

Thank you in advance!

[GenoMax]

tagging: Mason Meyer

K91 : You may also want to directly contact IGB developers.

Answer 1

[Mason Meyer]

Hello K91,

My name is Mason Meyer, IGB Support Specialist. I have seen the error you are referring to when no gene models are selected when trying to run ProtAnnot. The instructions below will allow you to select the gene so you can run ProtAnnot:

1. Choose the selection (arrow) tool.
2. Select the gene models you want to analyze by click-dragging a "rubber-band" over them.

Alternatively, you can click the introns in the gene models while holding the SHIFT key to select multiple genes.

Also, see: https://wiki.transvar.org/display/igbman/Selecting+Items

I hope this answer is able to help. Thank you for using IGB. Good luck on your thesis!