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RasmusKirkegaard edited this page Jan 27, 2015 · 8 revisions

Welcome to the AccessingGenbank wiki!

The on-line databases for biological sequence data are begging to be mined, but it is infeasible to do so manually. Even downloading the files is a hopeless task going through the web interfaces. Therefore I "mined" stackexchange for a solution.

What I was looking for was a python solution for:

  • downloading a list of Genbank files (automatically)
  • mining the Genbank files for a certain field (automatically)
  • Reporting a list of unique entries in the field

Why would you do this? To search for e.g. habitats where a certain group of micro organisms can be found.

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