daoudat

pyGeno has been recently ported to python 3. It allows you to play with genomes, proteomes, exomes, etc.. locally, in python and with a simple interface. You can use reference genomes or create you own (ex: patient specific) from a reference and sets of mutations.

It's available on github and pypi (pip install pyGeno)

Congratulations! ArangoDB is a great database.

100% the work of: http://www.sawssankaddoura.com/

Many thanks to the persons who submitted pull requests.

Actually it's not. It has been written from scratch including the ORM that runs in the background (https://github.com/tariqdaouda/rabaDB). The goal was to have a powerful optimized tool with 0 dependencies that can be easily deployed on any platform. It was designed to be flexible and powerful enough to be appealing to both bioinformaticians and casual users, and it used daily here at the Institute for Research in Immunology and Cancer (www.iric.ca) by professional bioinformaticians, as well as biologists who have learned to program using it.

PyGeno was already used for two peer reviewed articles:

-Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides. Granados, Sriranganadane, Daouda et al. 2014, Nat. Comm

-MHC I-associated peptides preferentially derive from transcripts bearing miRNA response elements. Granados et al. 2012, Blood

And four others are on the way.

Full doc: http://bioinfo.iric.ca/~daoudat/Mariana/

Thank you ;)