Could I apply this tool to other species?

[iaunicorn]

Hi,

As the title of your article said, gapseq could be used for the prediction of bacterial metabolic pathways. But I still would like to know whether this tool can be applied to other species, such as fungi.

Best,

[jotech]

Hi @iaunicorn,

so far we have support for bacteria and recently also archaea. I would say it depends on your demands, if you are just interested in the metabolic capacities of a fungal organisms without caring for compartments and special biomass, you could give it a try and maybe create a bacterial model from a fungi genome.

The pathway prediction works already for other organisms:
./gapseq find -p PWY-7118 -t Fungi Saccharomyces_cerevisiae.fna.gz

Let me know what you think about it!

[iaunicorn]

Hi jotech,

Thanks for your reply. I ran the command you mentioned：./gapseq find -p PWY-7118 -t Fungi Saccharomyces_cerevisiae.fna.gz
But I got an error: Error: Unknown argument: "qcov_hsp_perc". And then it showed the usage of tblastn.
I was confused about this error because my blast ran well. The version of BLAST is 2.2.29+.
I have no idea about how to solve this issue?

[jotech]

Do you mind opening the new issue for the blast problem? then this one can remain for the other species/fungi related question :)
(and please post the output of ./gapseq test)

[iaunicorn]

It doesn't matter to me. Thank you.