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Hi Arya,

Unfortunately we do not currently support the E.coli BW25113 genome assembly. Typically, an allele reference sequence source can be built for any species where there is an available DNA sequence (FASTA) file. The Convert Wizard that is available within the software can directly support conversion of the GTF formatted data. The Convert Wizard can be accessed by going to File > Add then clicking Convert in the lower left corner of the Data Source Library. Once the FASTA data is converted to TSF (Golden Helix annotation format) then it can be loaded into the GenomeBrowse plot window for visualization.

Let me know if you have any further questions.