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README.md

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auto_clone

This is a standalone python based server that intends to make the production of Gibson assembly primers & in-silico plasmids from that cloning more straightforward. In-silico plasmids are produced in GenBank (.gb) format with an eye toward proper integration with SnapGene. Appropriate insert annotations (assuming the sequences you input are CDSs) are produced in the resulting .gb file(s). Primers are output either in CSV format suitable for copy pasting, or 96-well plate tables in a Excel .xlsx, both formats suitable for direct oligonucleotide synthesis orders from IDT.

Dependencies:

  • Python3.6+
  • BioPython
  • Pandas
  • SciPy (for the Tornado stand alone webserver)
  • xlwt (for export of Excel file)

Installation (using MacPorts):

git clone https://github.com/photocyte/auto_clone.git
sudo port install py36
sudo port install py36-scipy
sudo port install py36-pandas
sudo port install py36-biopython
sudo port install py36-xlwt

Usage (Mac OS X):

sudo port select --set python3 python36
cd auto_clone
python3 ./auto_clone_server.py

Default webaddress is http://127.0.0.1:5686

See how_to_add_plasmids.txt to add plasmids.

Web-interface example:

GUI