Code for DNA plasmid editing.
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README.md

DNApy

This repo is currently broken. Efforts are underway to restore it and move to a development and deployment branch system.

A free and open source GUI toolkit for DNA editing - written in python

This project aims to provide a powerful codebase for viewing, editing and creating DNA in the GenBank format. The code is free to use, modify and re-distribute under a GPL license. Contributions in the form of improvements and new functions are welcome and encouraged!

The software is being developed on a Linux machine and works well in that environment. As the software matures testing will start on Windows and Mac to make sure it is cross-platform. The only external library that is needed is wxPython. Launch main.py to give the software a go (it is still under heavy development though).

Testing

To start testing the software you have to install python, wxpython and pycairo:

sudo apt-get install python2.7 python-wxgtk2.8 python-cairo

Then you can download the software and run it:

cd ~
git clone https://github.com/mengqvist/DNApy.git
cd DNApy
python main.py

Known problems

On Ubuntu 15.04 the following message might occure:

/usr/bin/xsel
Segmentation fault (core dumped)

This can be resolved by additionaly installing the package xclip:

sudo apt-get install xclip

DNApy GUI

Implemented Software features

  • Visualization of DNA sequence with sequence features

  • Plasmid view visualization

  • DNA editing, copy, paste, reverse complement

  • Unlimited undo/redo

  • Easy search for nucleotide or amino acid positions or sequence

  • Easy mutation by nucleotide or amino acid position (this one is pretty awesome!)

  • Design of mixed base codons for libraries

  • DNA translation to protein

  • Addition/removal/modification of genbank features

  • Addition/removal/modification of genbank qualifiers

Not Yet Implemented Software features (and priority list)

  • Analysis of sequence reads in the .ab1 format

  • Restriction enzyme finder

  • [done] located restrictionsites in dna
  • [partly] display restrictionsites in plasmid (missing zoom)
  • [todo] improve dna editor to visualise cut location
  • Addition/removal/modification of genbank header entries
  • [todo] improve genbank parser to allow parsing of corrupted genbank files from ApE, Serial Cloner, SnapGen Viewer
  • DNA codon optimization

  • Fetch genes/plasmids from NCBI

  • Primer design

  • Calculation of ribosome binding strength

  • NCBI blast for homologous genes

  • Simulate PCR

  • (Multiple) Sequence alignment