What kind of organisms are supported by gapseq?

By default gaspeq 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-seperated 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. SBML export needs the R package sybilSBML to be installed properly. In addition, final ouput 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 sybil or BacArena, the final output files are also kept in RDS format.