OrthoInspector

OrthoInspector is a specialized comparative genomics software suite written in Java that is used for the rapid detection of orthology and inparalogy relationships between species.

To set up and run the standalone package of OrthoInspector on Linux, follow this structured deployment guide: 1. Prerequisites & System Requirements

Before installing OrthoInspector, ensure your Linux system has the necessary environment and backend database tools installed:

Java Runtime Environment (JRE): Version 1.6 or higher is required to execute the compiled JAR files.

Database Management System: A background SQL server (PostgreSQL or MySQL) is needed to handle massive all-versus-all BLAST queries.

NCBI BLAST+: Preferably version 2.13.0 or later to handle sequence similarity searches.

C99 Compiler: A tool like gcc or clang for performance-dependent components.

Install the base system dependencies on Ubuntu/Debian via terminal:

sudo apt update sudo apt install default-jre postgresql ncbi-blast+ gcc Use code with caution. 2. Download and Extraction

The standalone software package is hosted by the Large-Scale Biology and Bioinformatics group (LBGI).

Download the OrthoInspector package archive using wget or curl: wget http://lbgi.fr Use code with caution.

Extract the files to your preferred installation directory (e.g., /opt or your local tool folder):

tar -xzvf OrthoInspector_suite.tar.gz cd OrthoInspector_suite/ Use code with caution. 3. Database Configuration

OrthoInspector does not run in complete isolation; it utilizes a background relational database to index sequence similarities and taxonomic paths.

Log in to your SQL prompt (this example uses PostgreSQL) and create a fresh database instance:

CREATE DATABASE orthoinspector_db; CREATE USER ortho_user WITH PASSWORD ‘securepassword’; GRANT ALL PRIVILEGES ON DATABASE orthoinspector_db TO ortho_user; Use code with caution.

Configure connections by opening the config.properties or database setup file inside the OrthoInspector folder and matching your SQL credentials (host, port, username, password). 4. Running OrthoInspector

The program is bundled into two main interface setups depending on your workflow pipelines: Mode A: The Graphical User Interface (GUI)

For interactive analysis, visualizing phylogenetic profiles, or exploring taxonomic distributions: java -jar OrthoInspector_GUI.jar Use code with caution.

Note: Ensure your Linux desktop environment (X11 or Wayland forwarding if using SSH) is active to pop open the interface framework. Mode B: Command Line Interface (CLI)

For heavy batch automation, parsing large-scale proteome data, or running high-throughput pipelines: java -jar OrthoInspector_CLI.jar -arguments Use code with caution. Common operational steps inside the CLI workflow involve:

Inference / Creation: Parsing your raw FASTA sequences and setting up local comparative tables.

Querying: Filtering specific orthology relationships by feeding sequence accession identifiers or taxids.

Are you planning to process your own custom genome sequences, or are you looking to cross-reference data using pre-calculated models from the OrthoInspector Web Portal? Let me know so I can tailor the pipeline commands for your exact workflow! orthoinspector – Arnaud Kress – ICube forge