Please suggest a suitable tool for GO annotation of a plant de novo assembled transcriptome

Question

[seta]

Hi all,

I conducted a de novo transcriptome assembly followed by doing blastx against nr database for a non-model plant. I imported the blastx results (xml format) into blast2go software for GO annotation, but it was very slow. I searched a lot on the net for alternative tools, but confused with many options. Please introduce me a suitable tool for this purpose, having your valuable experience with this task would be highly appreciated.

Thank you in advance

Answer 1

[Amitm]

Hi,

I am not sure if this would be the fastest method or most comprehensive, but I tried this strategy and here are the details. Both the tools involved can be run using multiple threads, so the time taken was reasonable -

1. First I did six frame translation of the de novo assembled contig sequences.
2. Then on a local nr blast database, I did blastp with the threshold of E-val <=10^-3
3. All contigs which showed hit at that level were selected
4. Then using a local installation of InterProScan, I scan the selected contigs for domain information.
5. Though local IPrScan didn't output GO mappings directly, but using this InterPro2GO ID mappings, I could obtain GO annotation

Probably there is a more elegant way of doing this but I thought this is a good start.