PhageBook

While bacteriophages are extremely abundant surprisingly little is known about them. PhageBook is a tool used to analyze and aid in the classification of bacteriophages.

Getting Started

• Clone the PhageBook repository git clone https://github.com/jblack332017/phagebook
• Install pip using the following instructions https://pip.pypa.io/en/stable/installing/
• Install PhageBook, run sudo pip install --editable . in the phagebook directory
• Ensure PhageBook is installed by running phagebook --help

Usage

Phagebook accepts a file containing a single bacteriophage capsid protein amino acid sequence in fasta format. Just like the following phiKZ.fasta:

>phiKZ MCP
MSVHALRELFKHKGEKNYEVFSMEDFIGRLESEIGLNDSVVSQG
RSLISSISHENFGTVQATDIQDAAAIYNKMQMLVNDYGFERVSSSDPQVRAREERVRE
NQITAATMAAIACADETKYIRALRGITKAKASNEDHVKVVQHQFNGPAGGIQVFENGV
GLENYNEKSQRDFRVVTIGYNLAASRQDEFAERIYPTTVINPIEGGVVQVLPYIAVMK
DVYHEVSGVKMDNEEVNMVEAYRDPSILDDESIALIPALDPAGSNADFFVDPALVPPY
TIKNEQNLTITTAPLKANVRLDLMGNSNANLLIQRGMLEVSDTIDPAGRLKNLFVLLG
GKVVKFKVDRLPRAVFQPDLVGDTRNAVIRFDSDDLVVSGDTTFIDGSADGVINDLKT
AKLSLRLSVGFGGTISLSKGDSKFGATDTYVDKVLNEDGQVMDNADPAVKAILDQLTD
LAVIGFELDTRFTNTNRRQRGHLLQTRALQFRHPIPMHAPVTLPMDTMTDEGPGEVVK
ALTVNTNIRNSNNAVKRMLNYLAQLREVVHNGYNRPKFGIIEGALSAVMRPTYRYKEL
DLEKVIDTIKSKDRWDDVCAAILNCVKAELFPAHRDSNIEAAFRVISGNQDETPMYLF
CSDKEIANYLMTKGDDRTLGAYLKYDIVSTNNQLFDGKLVVIPTRAVQQENDILSWGQ
FFYVSTVIADLPITRGGHQVTREIAAIPFNLHVNNIPFALEFKITGFQKVMGETQFNG
KLADLKP

PhageBook will then use blastp and the NCBI Entrata database to compile a a list of similar proteins and their corresponding Bacteriophage genomes.

PhageBook will run the resulting proteins through the multiple sequence alignment tool ClustalW and output the resulting alignment file proteins.aln

PhageBook will also generate a dotplot plot.png using Gepard

Commands

The basic PhageBook command is structured phagebook run <email> <path to protein fasta file>

Arguments

Arguments are required.

• email This is the email that will be reported to NCBI as part of PhageBook's queries
• protein fasta format This is the input protein that will be evaluated

Options

• --maxevalue Default: .15 - The maximum E value accepted during blastp
• --alignformat Default: clustal - The output of the alignment
• --blastp/--no-blastp Default: blast - Determines if blast will be run

A full command may look like the following:

$ phagebook --maxvalue 1.4 --no-blastp phagebook@example.com phikz.fasta

Results

The phagebook-results file will be generated in directory that you call PhageBook from:

- phagebook-results
  -- sequenceIds.txt
  -- proteins.fasta
  -- genomeIds.txt
  -- proteins 
    --- ... all protein fasta files
  -- genomes 
    --- full.fasta
  -- proteins.aln
  -- proteins.dnd
  -- plot.png

• proteins.aln is an alignment file that can be read by clustalx
• proteins.dnd is a dendrogram of the protein alignment
• plot.png is the dot plot generated by Gepard

Development

PhageBook is an open-source project that current supports Mac OS, Linux, and Windows. You are free to alter and use PhageBook. Please contribute and add new functionality and improvements.