FriPan

Interactive visualization of bacterial pan-genomes

Introduction

FriPan is a web-based tool for exploring the pan-genome of multiple bacterial genomes. FriPan does not perform the ortholog clustering itself, but it can import data from ProteinOrtho5 output files. Each isolate/strain is a row, and there is a columnar position for each gene cluster. You can zoom/scroll through the pan-proteome, and hover over sections to see a description of the gene.

Installation

Ensure you have npm installed:

brew install npm          # MacOS
sudo apt-get install npm  # Debian/Ubuntu
sudo yum install npm      # Redhat/Centos

Install the code and build:

git clone https://github.com/drpowell/FriPan
cd FriPan
npm install
make compile

Run the demo code locally using our Python-based server in server.sh:

./server.sh
firefox http://localhost:8030/pan.html

Or make it publicly accessible using your public_html if your server is already running Apache:

# will put in $HOME/public_html/fripan by default, type 'make help' to see options
make install
firefox http://localhost/~user/fripan/pan.html

Input files

An example set of input files with the stem test is provided:

1. test.proteinortho
2. test.descriptions
3. test.strains

XXX.proteinortho

This is the gene presence/absence matrix in TSV format. Each row is a gene ortholog cluster, and each column in a strain. Each cell in the matrix is gene ID, or * if none. Paralogs are CSV within the cell. The first 3 columns are unused, but you must use the exact names as below.

# Species   Genes   Alg.-Conn.   USA300    TW20      JKD6159
3           3       1            USA_001   TW20_001  JKD_001  
3           4       1            USA_002   TW20_002  JKD_002,JKD_004
2           2       1            USA_003   *         JKD_003 
1           1       1            USA_004   *         *

XXX.descriptions

This maps gene IDs from the strain columns, in 2-column TSV format.

USA_001	      DNA replication protein
USA_002       hypothetical protein
USA_003       gyrase A
USA_004       alcohol dehydrogenase (EC:1.1.1.1)
TW20_001      DNA replication protein
TW20_002      unknown protein
JKD_001       DNA replication protein, dnaA
JKD_002       hypothetical protein
JKD_003       gyrase
JKD_004       hypothetical protein

XXX.strains

This a multi-column TSV format. The first ID column links it with the strains in the other two files. The remainign columns can be used for colouring and ordering within the application.

ID        ST     Phenotype     Country    Colour
USA300    239    resistant     US         blue
TW20        2    suspectible   UK         green
JKD6159   239    resistant     AU         red

Viewing multiple pan genomes

The included example input files all start with the stem/prefix test. You can add as many pan-genomes to the fripan folder as you like, just give each of them a different stem, say mypop. Then you just append ?mypop to the URL, so it looks like http://example.com/~user/fripan/pan.html?mypop.

To simplify this, just add each stem to the file called pan.index. This will allow them to be selected via the Index menu item within the application.

Development

While developing code, it is useful to enable coffee in "watch" mode and with source maps. Run the following:

make debug

Issues

Report feedback, suggestions and bugs on the Issues page

Source

• Github: https://github.com/drpowell/FriPan
• Website: http://drpowell.github.io/FriPan/

Authors

• David Powell
• Torsten Seemann