I would like to extract all the GO terms associated to a set of transcripts. I want the go association of a plant species that is not included in biomart too. I know that I can use blast2go but it takes ages for a set of 40K transcript. I have also the blast of the transcripts. is there any fast way to get all the GO terms of each transcript in a standard method?
thanks a lot :)
I also have a headsup and question. I could manage to download the Uniprotkb association to all the GO terms. Since I use uniprotkb db for my blast, is it correct if I extract the GOs associated to the proteins as the hits of my blast? and if yes, how many hits I should consider?
Is it what blast2go and other similar softwares do?