What kind of organisms are supported by gapseq?

By default gapseq searches for pathways using bacterial sequences. This can be changed to other taxonomic ranks, for example to animals gapseq find -t Metazoa. The taxonomic rank should be compatible with uniprot because the respective sequences are download from uniprot. However, the reconstruction and gapfilling of metabolic networks is currently limited to bacteria and archaea.

What are the output files of gapseq?

Predicted pathways, reactions, and transporters are stored in tabulator-separated text files (.tbl) and the final metabolic network is saved as systems biology markup language (SBML) (.xml), which is an xml-based markup language for biological model exchange. In addition, final output and temporary files are stored in the R Data Format (RDS).

What are all these RDS output files for?

Temporary files are stored in R Data Format (RDS) and serve as input for other substeps such as gapseq draft, fill, or adapt. Since we propagate the further analysis with R using for example cobrar, the final output files are also kept in RDS format.