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

mengqvist / DNApy