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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,
The text was updated successfully, but these errors were encountered:
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
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?
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)
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,
The text was updated successfully, but these errors were encountered: