Question: Please suggest a suitable tool for GO annotation of a plant de novo assembled transcriptome
0
gravatar for seta
3.2 years ago by
seta1.1k
Sweden
seta1.1k wrote:

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, haveing your valuable experience with this task would be highly appreciated. 

Thank you in advance

go analysis annotation • 944 views
ADD COMMENTlink modified 3.2 years ago by Amitm1.6k • written 3.2 years ago by seta1.1k
1
gravatar for Amitm
3.2 years ago by
Amitm1.6k
UK
Amitm1.6k wrote:

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.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Amitm1.6k
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