I am focus on the plant and microbe interaction. The genome of this species had been released. I have the RNA-Seq data,how to find the GO ID with the GenBank Acc. No.;Uniprot Acc. No.; Pfam; KOG ?Thanks so much!
The obvious answer: align your reads to the transcripts, and use the annotation from them. If the transcripts are unannotated, align them to some dependable source (SwissProt, or KEGG), and derive the annotation you need from matches that you consider reliable. (You can e.g. use the GOA database that maps GO terms to UniProt, but mostly by automatic annotation, so the results may be questionable.)
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version 2.3.6
duplicate of http://www.biostars.org/post/show/1226
I think it depends what kind of microbes or plants he is using. Some of them are in the biomart repository, so it is possible to extract the data with he help of R, but not all of them.
For some of the annotations you can also try to use the DAVID interface. They have a new API tool. http://david.abcc.ncifcrf.gov/home.jsp or e-utils http://www.ncbi.nlm.nih.gov/books/NBK25501/ for queries against NCBI/ENTREZ
OK, I've reopened it.