Usage

The current version of BioCompass can network the gene clusters from ONE strain/genome against the gene clusters from NCBI/GenBank and MIBiG databases. Future Implementations will provide the option to analyze multiple strains.

Using BioCompass in your queried genome at your machine

If your installation of BioCompass succeeded, follow the instructions below. If not, please report an issue on our GitHub repo and include the error message you obtained during your installation.

  1. Submit your query genome to antiSMASH and “Download all results” (top right corner, icon shaped as a download arrow). If you don’t have a sample for testing, feel free to use the strain Moorea producens PAL 15AUG08-1 and its antiSMASH result;

  2. Once you downloaded the files, descompress and save them into a folder named for example “antiSMASH_input”. We advise renaming the subfolder inside antiSMASH_input to a shorter name representing your strain. As an example for this tutorial, since we’re using the genome of Moorea producens PAL 15AUG08-1, we’ll rename the subfolder to “PAL”;

  3. Download multigeneBLAST 1.1.14 for command line;

  4. Now, execute BioCompass using the following comand:

    cd path/to/BioCompass/BioCompass
make INPUTDIR='path/to/antiSMASH_input' REFNAME='NAME' MULTIGENEBLASTDIR='path/to/multigeneblast' ALL

For our example, using Moorea producens PAL 15AUG08-1 and assuming that both antiSMASH_input and multigeneBLAST are in the main BioCompass folder, the command should look like:

make INPUTDIR='/home/Desktop/BioCompass/antiSMASH_input' REFNAME='PAL' MULTIGENEBLASTDIR='/home/Desktop/BioCompass/multigeneblast_1.1.14_macosx_commandline' ALL

PS: the folder name inside antiSMASH_input and the REFNAME must be the same!

  1. Select the cutoff you would like to use for filtering your results. We advise using a low cutoff first, checking the network diagram and then revisiting this step using the code below (that only reruns this step, not the whole pipeline) to find the best cutoff for your data:

    make ???

  2. The table outputs (REFNAME_edges.txt and REFNAME_nodes.txt) can be vizualized as a network diagram using Cytoscape 3.2.1, according to the tutorial here (tutorial under construction!)

PS2: The running time of BioCompass at an average laptop (e.g. MacBook Pro 2.6 GHz Intel Core i5 8 GB 1600 MHz DDR3) for Moorea producens PAL 15AUG08-1 (which contains 44 gene clusters) was approximately 7 hours. We advise the use of the command screen.

Using BioCompass in your queried genome at Amazon Web Service

We expect that the tutorial above would work at your machine, but in case it doesn’t, we can garantee that it will work on AWS if followed the instructions below. The instructions for running BioCompass at AWS are very similar than explained in the tutorial above, although requires the following setup first.

(Tutorial under construction)

Using BioCompass in your project

To use BioCompass in a project:

import BioCompass