How to analyze GO annotation?

[SES]

You could try InterProScan, which will allow you to annotate your genes, and it will return GO terms with your annotations.

[phoss]

Hi henry_by,
If I'm not mistaken, EBI has GO annotations embedded in some fasta headers. You may want to look into creating a local blast-instance of these files and locally-blast your predicted genes against it. You can then simply parse such hits and extract out the respective GO from the header... shouldn't take very long for your 11k genes.

[henry_by]

Thank you for your suggest. I have construct a draft map for an eukaryotic animal. By the gene predict software, like exonhunter, I have received nearly 11000 genes among this whole genome. Now, I want to use these fasta sequences (predict genes) to receive corresponding Go annotation. I have tried the blast2go on the net service, however it is very slowly. It will spend 2 weeks in annoting 11000 genes. Do you know some more efficient software can complete this task?

[ETHANol]

You definitely need to be more specific about your experiment, what you have done and what you want to do. Questions like these never lead to good answers. 'Genome analysis' is what?

[henry_by]

I first perform genome analysis, and predict many genes. I don't know how to perform Go analysis. I have try the blast2go on the net service, however it is very slowly. Can I used other located software to complete this task? look forward your help.