Informed curation and gapfilling of metabolic networks
- Needed input files
- Genome (fna)
- Draft model (xml)
- Seed database corrections
- python3 src/seedcorrect.py dat/myb71.xml
- Obtaining candidate reactions
- ./gapseq.sh -p core dat/myb71.fna
- ./gapseq.sh -p degradation dat/myb71.fna
- ./transporter.sh dat/myb71.fna
- Gapfilling
- Rscript gf.suite.R -m ./dat/myb71_corrected.xml -c ./dat/myb71-core-Reactions.lst,dat/myb71-degradation-Reactions.lst,dat/myb71-Transporter.lst -n dat/media/TSBmed.csv