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Question: Where to download gff3 file for EcoCyc data?
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gravatar for O.rka
3.0 years ago by
O.rka • 230
O.rka • 230 wrote:

I'm looking for a gff3 file with EcoCyc IDs. Do I need to just download the version from Ensembl and then convert the IDs? Alternatively, is there a flat file from EcoCyc that has the positions of all of the genes in E. coli?

ecoli genes assembly gff3 • 1.2k views
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modified 2.9 years ago by tdmurphy • 190 • written 3.0 years ago by O.rka • 230
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2.9 years ago by
tdmurphy • 190
tdmurphy • 190 wrote:

I think EcoCyc uses the same IDs as EcoGene (EG#####), which are available on the GenBank and RefSeq annotations at NCBI. Try the "Download" links at the right from this page: https://www.ncbi.nlm.nih.gov/assembly/GCF_000005845.2

Both GFF3 and flatfiles are available.
ADD COMMENT • link written 2.9 years ago by tdmurphy • 190
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