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

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

go-analysis annotation
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updated by Ram Ram • written by seta seta

1 answer

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.

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updated by Ram Ram • written by Amitm Amitm

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