Hi, the important step to analyze transcriptome data is the functional enrichment, of which GO and KEGG is the most popular. My question is how to assign the GO or KEGG numbers to my bacterial genome? I'd like to do that with my own computer, not online tools. Any suggestions will be appreciated.
Dear Mingju Hao , if you are interested to assign GO or EC number to your sequences, you can use different procedures, all based on sequence similarity searches. You can perform an InterProScan analysis, retrieving for each query sequence also the GO or EC number and related pathways, or you can perform a BLAST versus UniProt search, retrieving the UniProt ID and then performing a match (in UniProt database) between that ID and the GO or EC number associated to that ID. Both tools are available for download:
https://www.ebi.ac.uk/interpro/download/
https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Luca Ambrosino Peter Karlskov-Mortensen
Thanks for your help. InterProScan works well to assign GO number. It looks like KOBAS is good at assigning KEGG number. I will have a try.
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