Dear all I have 3652 gene's ids as well as corresponding protein ids of a bacterial genome. I need to annotate these sequences in terms of their pathway. I have used BLASTKOALA , KASS, DAVID and geneSCF for tis purpose, but the problem is only 50% sequences are annotated using KASS and BLASTKOALA. As the 50% annotation is of no use, is there any other tool by which I can annotate my protein sequences for their pathway analysis.
Why BLASTKOALA assigns KO numbers to few genes? is there any parameters we need to set?Did I do any mistake ? Is there any parameters we need to set while implementing BLASTKOALA? I can not go ahead with the 50% pathway annotation. kindly tell me other methods or tool for this purpose.