Do you have any idea how to merge eggnog and interproscan (e.g. Pfam and Go columns). I realized that Interproscan does produce less Pfam entry per gene than eggnog does. I know eggnog is orthologous database, however I would expect that Interproscan have more protein matches with the input data as It is a kind of protein database.
Concerning the second point, There are some content differences per gene, for example eggnog says the gene has two Pfam, (pfam0001,pfam0002) and interproscan says (pfam0001,pfam0002, pfam0003). In that case, If I merge these information into one column and can I still use same gene names produced by eggnog?
The last point is that taxonomy. If I use another tool for taxonomy assignment, can I replace assignment, which is produced by the external tool, with eggnog taxonomy assignment but provided the other columns (gene IDs, COG categories) remain same?
Thank you !
The question is, do you think is a good idea to mix results from different DBs? As you know, EggNOG uses orthologous to infer functions, while Interpro uses motifs. Therefore, they would not necessarily produce the same results. Which is the best? I don't think there is an answer, it might depend on your specie/species. If you're doing this for a few genes, you can inspect the results manually, otherwise, it will be difficult to get accurate results if you mix them.
Yes, It is good point, @buffo. Actually, I know these use different database and also have different approaches. However, eg. blast2go does merge GO IDs result from these two tools. Also, ENTAP does do that. Blast2Go and ENTAP also runs blast apart from Interproscan and eggnog.
I am just wondering how they can handle the result in the final table. The case could be metagenomic data.