How To Generate A Simple Isoform Diagram

Question

[Zak]

Hello folks, I'm doing a presentation for a summer program at the end of the week and I am having some trouble making diagrams.

I'm not very artistically talented, but I need to somehow include a diagram of several isoforms for a particular gene I was studying. I don't really want to mock them up in powerpoint, and nothing else I've tried has worked. The output from the UCSC database is just too large and complicated (I really just want chart of which exons are in which isoforms), and won't present well.

I have tried using GenomeTools, but unfortunately I can't compile the tool on the office computer and I can't even get the GFF3 file to parse correctly for the online tool.

Does anybody know how I can do this?

Thanks!

Answer 1

[Ido Tamir]

UCSC genome browser. hide all. Genes and Gene Prediction tracks| UCSC Genes: full. Export as PDF/PS on top right. Open in Inkscape and modify.

IGB Genome browser, load genome, zoom in to gene. save as PDF. Open in Inkscape and modify.

Answer 2

[Arun]

In this paper, they show something called "splice graphs". Maybe its of interest to you?

Answer 3

[Mary]

Two handy little tools I've used for simple diagrams are MyDomain at Prosite: http://prosite.expasy.org/mydomains

And I have always loved the Model Maker at NCBI, but I think I'm the only person that ever used it... And as far as I know you can only get to it from within MapViewer. So you have to go to your gene in Map Viewer, show the "genes on sequence" map, then click the mm link, and then you can assemble your favorite patterns.

Here's an example: http://www.ncbi.nlm.nih.gov/projects/mapview/modelmaker.cgi?taxid=9606&contig=NT_004610.19&gene=ZNF593 {hope that works for other people}

At the bottom you can choose which exons to show or not show, and create little models.