Extract CDS product from Genbank file with coordinate range

Question

[obywanw]

Hi, I am trying to extract the CDS product name from a Genbank file using coordinate range. In short, I have coordinate matching inside a gene in the Genbank file (coordinate 5679-57699) I want to use this to retrieve the product name (gene product with coordinate 5450..6789). I have to do that on several Genbank files (merged in one). What would be your suggestions ?

thanks for your help,

Cedric

Answer 1

[vkkodali_ncbi]

You can use Entrez Direct for this if you are working with public data. You can query the Entrez database, download the GenBank flat file in XML format and parse it using the xtract command. You should be able to find some sample code in Biostars.