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guillecg
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mars-biofoundry
Metabolic engineering towards a biofoundry on Mars
MIT License
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PoC: Pipeline for retrieving rules for a given organism
#12
Closed
guillecg
closed
1 year ago
guillecg
commented
1 year ago
[x] Select organism with sequenced genome
[x] Retrieve
EC numbers
from DBs:
[x] ~BioCyc~ (paid account required)
[x] KEGG (via
bioservices
)
[x] Query RetroRules for the given EC to create the
rules.csv
file
[x] Done by downloading the
RetroRules pre-parsed reaction rule CSV file
and merging previous data on EC numbers
guillecg
commented
1 year ago
BRENDA has limited but manually curated information.
EMBL-EBI's Enzyme Portal is a secondary information resource, so data retrieved must be used carefully.
ExPASY's ENZYME service cannot be queried by organism AFAIK.
guillecg
commented
1 year ago
Closed as per 1eb07c5