Gene Ontology in non-model organisms

[nr23]

I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have 2 options:

- BLAST my DE genes against a database with GO terms (human/mouse) to look for orthologs
- Use a program that assigns GO from BLAST results, such as Blast2GO

I've been trying with Blast2GO recently, but find if very slow and generally lacking - does anyone have any experience doing GO in Xenopus or other non-model organisms?

[Birdman]

I also tried Blast2Go without success using a non-model organism. After countless hours I gave up, since it was messing up my blast results IDs and at the end it was not even retrieving GO terms properly.

Finally, I did the annotation with Trinotate and it went very smoothly. The steps are well described on the website. You need blast results as an input.

Good luck with your analyses.

[amolkolte]

InterProScan followed by BiNGO

blast2go is on the verge of getting commercialized (as they have started selling PRO versions) and my previous experience was not so good with it. I used IntrProScan to associate GO terms with the transcript sequences. It was a long run but it also reported all the possible sequence features.

To use these custom annotation was tricky for visualization, but thanks to BiNGO, I was able to do it flawlessly. For future use I have documented it here, http://infoplatter.blogspot.in/2014/...alysis-in.html