Hi Biostars forum
I have a de novo transcriptome annotated mainly against SwissProt, so I have contigs ==> UniProt accession codes. Using the UniProt conversion tool I can obtain GO and also KEGG which corresponds to the UniProt accession, but obviusly I have obtained matches against different organisms. My desired next step consist in to map my KEGG codes in to pathways, but the KEGG mapping tool ask about "org" code and I can't obtain a "global" result if I have to select my matching organisms one by one. I was looking for a solution googling and using the forum search tab but I can't find anything.
As an example:
bta:540248 hsa:51202 mcc:574295
I can search 1 by 1 if I use the organisms code, but I cant map them together. Is that possible?? or I need to find orthologous in just one species??
In some papers focused around non-model organism I have read in M&M section the use of KOBAS to perform KEGG pathway analysis. However, when I have tried this resource I found the same problem, I have to specify one species when my annotation file contains SwissProt IDs coming from different species. I know if I do not specify one species, KOBAS takes human by default. Maybe these authors miss used KOBAS and have analysed their data just for the transcripts with hits against human?? I have missed something about KOBAS usage??
Please give me some wisdom tips, thank you