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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?

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interesting question, but no experience doing this from me. Have you tried BioStars.org? –  Luke Feb 14 at 15:40
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2 Answers

I've done a functional annotation of a non-model, and used Blast2Go with fine results.

Specifically, I took all of my proteins and queried again the NCBI non redundant (nr) protein database using mpiBLAST, then I analyzed this output using Blast2GO (B2G4PIPE) and a local B2G Database.

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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 transcripts, it ran long but it 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/2014/04/gene-ontology-go-enrichment-analysis-in.html

Good luck!!

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