NPACT (N-Profile Analysis and Computation Tool) implements methods to identify in nucleotide sequences regions of statistically-significant compositional three-base periodicity associated to ORF structures, to compare the newly-identified ORFs with pre-annotated collections of genes and to highlight potential new genes not included in the annotation. The primary output is a graphical representation of sequence features represented by frame-specific compositional profiles (by default, GC content) and sequence segments with significant periodicity (Hits) together with representation of the pre-annotated genes and, in a separate track, newly identified ORFs not included in the annotation.

NPACT accepts input sequences of any length and its dynamical graphical representations allow easy browsing and analysis of an entire prokaryotic genome.

This NPACT project was developed in 2011-2015 by Acceleration.net under contract from Luciano Brocchieri at the University of Florida Genetics Institute based on sequence-analysis methods and computational tools developed by Luciano Brocchieri at the University of Florida Genetics Institute.

This project is primarily meant to be used as a website (See the npactflask component). The pynpact component can be used directly on the command line though this has not been tested recently.

The required libraries are packaged with this project as much as possible to make it easier to get started and more resistant to external changes.

You will need Python and Make on your system before getting started. See requirements.md for more information.

1. run bootstrap.py to get everything going.

    python bootstrap.py
   

If that completes successfuly then you should see "Successfully finished bootstrap.py". If it doesn't, the rest won't work.

There is a development webserver bundled in that will help for local development. To use:

1. source ve/bin/activate[.csh]
2. npactflask/bin/devserver
3. open http://127.0.0.1:5000/npact/

NB: Apache normally runs as a different user and you may encounter permissions issues if you run the development server in the same directory that has been served under Apache.

To log in to the npact management page, the user is npactmanager

The password should be located in .htpasswd file in the webroot e.g. from the apache.conf:

authuserfile /var/www/html/genome.ufl.edu/npact/.htpasswd

The project was developed with this in mind but has been extended beyond it so there is no good way to provide detailed configuration via the command line--it's only available via the website. This is still useful to run the analysis with all the default options.

1. In a shell from the project root activate the virtualenv: . ve/bin/activate
2. pynpact <gbkfile>
3. It will print a message reporting the output.

In the root of the project are several configuration and build files.

• requirements.txt - the list of python packages that are used. Most of the referenced packages exist in the lib folder; the rest are described below.
• apache.conf - sample apache configuration (and what's actually used on genome.ufl.edu)
• bootstrap.py - the script that helps get a new checkout of the project running. Run this after a fresh checkout to get the virtual environment and dependencies setup.
• publish.sh - used for publishing to genome.ufl.edu (or potentially another host)
• lib/ - contains the libraries this project depends on.
• ve/ - holds the python virtual environment-- won't exist until after bootstrap.py has been called. Can be deleted and recreated with boostrap.py at any point.
• webroot/ - a container for the dynamic portion that will change while running as a website. Uploaded files, logs, daemon pidfile, and deferred tasks are all written underneath here.

For Python N-Profile Analysis and Computation Tool. This is the main module that interacts with Genbank files to compute the graphs of N-Profile ratios.

The C code at pynpact/src does most of the analysis and the python code in pynpact/pynpact helps glue it together into an easy-to-run process.

• pynpact/pynpact/parsing.py this is used to investigate a GBK file and come up with the default options that will be used on a run. To change the default analysis options.on the websites run page, go here. To change the help text about one of the options, go here.
• pynpact/pynpact/entrez.py is used for querying entrez to find gbk files.
• pynpact/pynpact/main.py actually coordinates the running of the C programs and produces the PS output.

This is the code for the website. It is built on top of Flask. See npactflask/README.md.