A database for all histone proteins in NR organized by their known non-allelic protein isoforms, called variants. This resource can be used to understand how changes in histone variants affect structure, complex formation, and nucleosome function. For more information, please read our paper (citation below).

The database can be accessed at http://www.ncbi.nlm.nih.gov/projects/histonedb/

• Python 2.7
• Flup 1.0.2, if using fastcgi
• Django 1.8
• django-extensions 1.5.3
• MySQL-python 1.2.5
• BioPython 1.65
• colour 0.1.1
• HMMER 3.1b2
• BLAST+
• EMBOSS

If you want to test the server on your own machine, you must make sure have all of the dependencies listed above and follow these steps.

1. Create MySQL database, and store the login information in HistoneDB/NCBI_database_info.py, which is formatted in the following way:

#This file contains the user name and password for the HistoneDB 2.0
#Keep hidden
name = "DB NAME"
user = "DB USER"
password = "DB PASS"
host = "DB URL"

2. Build NCBI Taxonomy with djangophylocore

python manage.py buildncbi
python manage.py loadtaxonomy
python manage.py buildtaxonomytoc

3. Classify sequences in NR

python manage.py buildvariants

4. Build trees from seed sequences

python manage.py buildtrees

5. Build organism sunbursts for each variant

python manage.py buildsunburst

6. Build MSA and GFF sequence features for variants

python manage.py buildseedinfo

You have several options to run the Django server. The easiest way is to run it through manage.py, specifying a port (we use port 8080 in the example):

python manage.py runserver 8080

For deployment, we use FastCGI on the NCBI webservers. While this will be deprecated in the next version of Django, it is what NCBI allows. For more info, please read https://docs.djangoproject.com/en/1.8/howto/deployment/fastcgi/

Coming soon.

• Eli Draizen
• Alexey K. Shaytan
• Anna Panchenko
• Leonardu Marino-Ramirez
• David Landsman
• Paul Talbert