Protein Functional Annotations

Question

[Rahul Sharma]

Dear all,

I have predicted genes (both homology and ab-initio based methods were used) after the genome assembly of a fungal genome. Using OrthoMCL, orthologs within the four genomes (Well annotated and valid proteins) were obtained and functions were assigned. Later I ran the InterProScan and Pfam for further confirmations and functional annotations. I have following questions:

1). I want to identify/count the KOGs in the generated protein sequences, I downloaded KOGs from ftp://ftp.ncbi.nih.gov/pub/COG/KOG/. Should I blast these KOGs locally and use the information for estimating the KOGs in the predicted genes/proteins?

2). Ho to find the GO information, should I use InterProscan GO information?

3). How to use KEGG locally on my machine, Is it paid? Can I download and use it locally?

4). Any other method or tool to assign functions to computationally predicted genes?

I would really appreciate your suggestions.

Thnx, Rahul

[User000]

Hi, I would like to ask you how did you predict genes, could you please describe both ways a little bit in details? thank you..

Answer 1

[qiyunzhu]

Here's a software designed for you: blast2GO

http://www.blast2go.com/b2glaunch/start-blast2go

It's so easy to use. Simply click it open and you will know what to do.

[Rahul Sharma]

Thanks for your reply. Actually I have around 6000 sequences, I think it is not possible to automate Blast2GO on unix based machine. If you have experience in handing this much of sequences with Blast2Go please let me know. Thanks in advance.

[qiyunzhu]

Hello, I'm glad to share what I know about this software. Blast2Go does not require expensive computational resource. You can simply run it on your personal computer. All you need is memory. The more the better! I suggest 8 GB+ for your 6000 sequences. If your laptop does not have many memory plugged, then you can split your 6000 sequences into several parts and run separately. If you do want to run Blast2Go on your unix-based machine, does it have some sort of graphic interface? If so, I think you can find out a way to execute Blast2Go, because it simply needs java. I have managed to run it in Windows, Mac and Ubuntu. If you need specific instructions please let me know.