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jotech
How to get more carbon sources or fermentation products in fill step?
Hi again, I tried the new function of prediction of carbon sources and fermentation products, and it is useful for me. I can get two lists of the same kind of 186 carbon sources or fermentation products. Can I add more carbon sources or fermentation products in this step? I don't know which is the key file. Thanks! Best, Erique
Hi Erique,
could you provide some more detail on what you would like to achieve? Are you referring to the gapseq medium module to predict a gap-fill medium? At what stage of the gapseq workflow do you want to add additional carbon sources?
just to add to add shortly: candidate carbon sources and fermentation products are listed in: https://github.com/jotech/gapseq/blob/master/dat/subex.tbl
Hi @Waschina, In the last step (gapseq fill), I use the new function (-w) to get the information of carbon sources and fermentation products. But many carbon sources that I want to explore are not on the list. So, I want to add more targets to the results. I will add some carbon sources in dat/subex.tbl as @jotech suggested. Thanks a lot. Best, Erique
Hi @Erique29 do you mind to share which carbon sources are missing? Maybe we can add them so that they could be found by default
Hi @jotech , Sure, I check subex.tbl, some carbon sources from BIOLOG test were not included. Like,
- β-Methyl-D-Glucoside EX_cpd11603_e0
- N-Acetyl-β-D-Mannosamine EX_cpd27563_e0
- D-Fucose EX_cpd00750_e0
- D-Fructose-6-PO4 EX_cpd00072_e0
- Gelatin EX_cpd11879_e0
- D-Malic Acid EX_cpd00386_e0
- D-Aspartic Acid EX_cpd00320_e0
- Glycyl-L-Proline EX_cpd22832_e0
- Acetoacetic Acid EX_cpd00142_e2
- Methyl Pyruvate EX_cpd24420_e2
- D-Lactic Acid Methyl Ester EX_cpd24428_e2
- 3-Methyl Glucose EX_cpd26351_e2
- L-Galactonic Acid Lactone EX_cpd00820_e3
- p-Hydroxy-Phenylacetic Acid EX_cpd00489_e3
- Bromo-Succinic Acid EX_cpd23859_e4
- γ-Amino-Butryric Acid EX_cpd00281_e5
- β-Hydroxy-D,L Butyric Acid EX_cpd02042_e6
Can I ask another question? There are 369 candidate carbon sources and fermentation products in the list. But there was only part of them shown in the cs.tbl and ferm.tbl. How can I get the full list? Thank!
Best