Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/deprekate/PHANOTATE
PHANOTATE: a tool to annotate phage genomes.
https://github.com/deprekate/PHANOTATE
annotate-phage-genomes annotation genomics phage
Last synced: about 1 month ago
JSON representation
PHANOTATE: a tool to annotate phage genomes.
- Host: GitHub
- URL: https://github.com/deprekate/PHANOTATE
- Owner: deprekate
- License: gpl-3.0
- Created: 2017-05-16T21:30:09.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2024-02-29T23:41:18.000Z (4 months ago)
- Last Synced: 2024-04-04T07:02:56.136Z (3 months ago)
- Topics: annotate-phage-genomes, annotation, genomics, phage
- Language: Python
- Homepage:
- Size: 1.33 MB
- Stars: 64
- Watchers: 10
- Forks: 7
- Open Issues: 12
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Citation: CITATION.md
Lists
- awesome-phages - PHANOTATE - PHANOTATE is a tool to annotate phage genomes. It uses the (Annotation / Gene prediction-annotation)
README
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
```sh
git clone https://github.com/deprekate/PHANOTATE.git
pip3 install PHANOTATE/.
```
PHANOTATE Example
--------------
Run on included sample data:
```sh
phanotate.py tests/NC_001416.1.fasta
```
Output is the predicted ORFs, and should look like
```sh
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:
```sh
$ 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:
```sh
$ 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:
```sh
$ phanotate.py tests/phiX174.fasta -f faa | head -n2
>phiX174_CDS_[100..627] [note=score:-4.827981E+02]
MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK*