phanotate 1.6.6

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
 pip3 install PHANOTATE/.

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    +
...

PHANOTATE has the ability to output different formats: genbank, gff, gff3, fasta

Output a genbank file that contains the genes and genome:

$ phanotate.py tests/phiX174.fasta -f genbank | head 
LOCUS       phiX174                 5386 bp 
FEATURES             Location/Qualifiers
     CDS             100..627
                     /note=score:-4.827981E+02
     CDS             687..1622
                     /note=score:-4.857517E+06
     CDS             1686..3227
                     /note=score:-3.785434E+10
     CDS             3224..3484
                     /note=score:-3.779878E+02

Output the nucleotide bases of the gene calls in fasta format:

$ phanotate.py tests/phiX174.fasta -f fna | head -n2
>phiX174_CDS_[100..627] [note=score:-4.827981E+02]
atgtttcagacttttatttctcgccataattcaaactttttttctgataagctggttctcacttctgttactccagcttcttcggcacctgttttacagacacctaaagctacatcgtcaacgttatattttgatagtttgacggttaatgctggtaatggtggttttcttcattgcattcagatggatacatctgtcaacgccgctaatcaggttgtttctgttggtgctgatattgcttttgatgccgaccctaaattttttgcctgtttggttcgctttgagtcttcttcggttccgactaccctcccgactgcctatgatgtttatcctttgaatggtcgccatgatggtggttattataccgtcaaggactgtgtgactattgacgtccttccccgtacgccgggcaataacgtttatgttggtttcatggtttggtctaactttaccgctactaaatgccgcggattggtttcgctgaatcaggttattaaagagattatttgtctccagccacttaagtga

Output the amino-acids of the gene calls in fasta format:

$ phanotate.py tests/phiX174.fasta -f faa | head -n2
>phiX174_CDS_[100..627] [note=score:-4.827981E+02]
MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK*