Hi,
I would like to annotate blast results performed with diamond blastx using Blast2GO. I was apparently able to load sequences and blast results into blast2GO (--outfmt 5 in diamond). Things seem to appear normally in the table and in Blast result menu.
However, it seems I can't perform the next step which is mapping blast results to GO. The button "mapping" in the menu is unavailable and appears grey. I can't even run the process.
I am sure there is a very simple answer to this issue but I haven't been able to find an answer on forums. I am using Blast2GO Basic so maybe the function is not available, but I assumed from the documentation that it was possible to perform the whole annotation procedure in Blast2GO even with this version.
Thanks for the help
H
can you confirm that you used the correct output format of blast (/diamond, xml if I recall correctly) and the correct database (== one that blast2go also knows of) ?
I thought so. Database and output options were : (outfmt 5 corresponds to diamond xml format)
Example of one blast result inport in B2GO :
So apparently Gene identifier and Xref are missing, import was maybe not as successful as I thought. Looking at my xml file, db number is : 287467303
I don't really know how to fix this though.
you can run a small test with the 'normal' NCBI blast and see if that works?
Don't recall now but I'm not sure that 'nr' is an accepted DB for blast2GO ?
Yes , I tried using 'normal' blast both against nr and uniprot and it didn't change anything.
It is strange because, looking at blast2go video tutorial, the button seems to be available even when only a fasta file is loaded which is not the case here.
To me, it seems that mapping is just not supported by my Blast2GO version (Blast2GO Basic). It is puzzling because it is stated here that Basic version supports GO annotation :
https://www.blast2go.com/b2glaunch/resources/36-tutorialblastall
Or, annotation is available but not mapping (which doesn't make any sense given mapping is required for annotation).
I'm running out of ideas here I must admit.
Maybe there is just no info on your hits in the blast2GO mapping table? would be a bit weird though that none give some info. Perhaps you can run a small test with a protein that you know should get some info (has some GO assigned to it)?