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.