phanotate 1.3.1

A a tool to annotate phage genomes

Introduction

PHANOTATE is a tool to annotate phage genomes. It uses the assumption that non-coding bases in a phage genome is disadvantageous, and then populates a weighted graph to find the optimal path through the six frames of the DNA where open reading frames are beneficial paths, while gaps and overlaps are penalized paths.

To install PHANOTATE,

pip3 install phanotate

or

 git clone https://github.com/deprekate/PHANOTATE.git
 cd PHANOTATE
 python3 setup.py install

The current version of PHANOTATE relies on C binary "FastPathZ", from the project FastPath, to calculate the optimal path quickly.

PHANOTATE Example

Run on included sample data:

./phanotate.py tests/NC_001416.1.fasta 

Output is the predicted ORFs, and should look like

125     187     +
191     736     +
741     2636    +
2633    2839    +
2836    4437    +
4319    5737    +
...