After running Gene Finding within Blast2GO I ended up with a GFF containing the genome coordinates and also a Blast2GO project.
With the project, I can run the full functional annotation steps Blast, InterProScan, Mapping and Annotation.
Now it would be nice if I could export a GFF file retrieved from Gene Finding containing the GOs from the annotated project.
This is possible with Blast2GO PRO.
To export the GFF with the GO terms first, make sure you have both GFF and Blast2GO projects saved as .b2g and do the following:
- Open the Gene Finder GFF output.
- Go to File > Export > Export GFF.
- Export parameters window will open (Figure 1).
- Select the output folder where to save the .gff file
- Select the type GFF3 and GFF2/GTF
- Features to Export (e.g. gene, CDS, mRNA, exon)
- Choose to export header, Fasta
- Add GOs from Project – this is the option that has to be enabled to add the GOs from project to the GFF file.
- Blast2GO Project – provide the saved project that contains the functional annotation steps
- Add GOs to Type – which features type will have the GOs (e.g. CDS)
- Match Sequence Name to Attribute – the attribute column from the GFF jas to match the Sequence Name column of the project.
- Click Export – the GFF file will be generated containing the GO ids from the Project.
With the above-mentioned instructions and these files, you will be able to export a GFF file containing the GO terms from the Blast2GO project.