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).
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
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
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Visualization of DNA sequence with sequence features
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Plasmid view visualization
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DNA editing, copy, paste, reverse complement
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Unlimited undo/redo
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Easy search for nucleotide or amino acid positions or sequence
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Easy mutation by nucleotide or amino acid position (this one is pretty awesome!)
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Design of mixed base codons for libraries
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DNA translation to protein
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Addition/removal/modification of genbank features
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Addition/removal/modification of genbank qualifiers
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Analysis of sequence reads in the .ab1 format
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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
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DNA codon optimization
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Fetch genes/plasmids from NCBI
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Primer design
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Calculation of ribosome binding strength
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NCBI blast for homologous genes
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Simulate PCR
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(Multiple) Sequence alignment