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PROBESt Web Application

A web-based interface for the PROBESt probe generation and optimization tool.

Features

  • User-friendly web interface for all PROBESt parameters
  • File upload for input FASTA, BLAST databases, and contig tables
  • Real-time processing with progress indicators
  • Results visualization showing top 5 best probes
  • Download results as a ZIP file containing all output files

Installation

  1. Install Flask and required dependencies:
pip install flask werkzeug

  1. Ensure all PROBESt dependencies are installed (see main README.md)

  2. Make sure primer3_core and blastn are available in your PATH

Running the Application

From the project root directory:

cd app
python app.py

The application will be available at http://localhost:5000

Usage

Required Inputs

  1. Input FASTA File: Input FASTA file for probe generation (.fna recommended)

    • Can be a single FASTA file (.fa, .fasta, .fna) or an archive (.zip, .tar.gz) containing FASTA files

  2. True Base Archive: Archive containing FASTA files for primer adjustment

    • Must be a .zip or .tar.gz archive
    • Archive should contain one or more FASTA files (.fa, .fasta, .fna, optionally gzipped)
    • The archive will be automatically preprocessed using prep_db.sh to create a BLAST database

  3. False Base Archive(s): Archive(s) containing FASTA files for non-specific testing

    • Must be .zip or .tar.gz archives
    • Can upload multiple archives
    • Each archive will be automatically preprocessed using prep_db.sh to create BLAST databases

Note: The contig table is automatically generated from the true base archive during preprocessing.

Optional Parameters

The web interface provides access to all optional parameters:

  • Basic Parameters: Threads, Algorithm type
  • Evolutionary Algorithm: Iterations, mutation rates, set sizes
  • Primer3 Parameters: Primer size ranges, product size
  • BLAST Parameters: Word size, scoring parameters
  • Probe Check Parameters: Mismatch thresholds, identity requirements

Results

After processing:

  1. Top 5 Probes are displayed on screen with:

    • Probe name
    • Hit count (number of matches)
    • Sequence length
    • Full sequence

  2. Download Results button provides a ZIP file containing:

    • output.fa: Final probe sequences
    • stats.csv: Iteration statistics
    • All intermediate files from the pipeline

File Structure

app/
├── app.py              # Flask application
├── templates/
│   └── index.html     # Main web interface
├── static/
│   ├── style.css      # Styling
│   └── script.js      # Client-side JavaScript
├── uploads/           # Temporary file uploads (created automatically)
└── results/            # Processing results (created automatically)

Notes

  • Uploaded files are stored temporarily and cleaned up after processing
  • Processing may take several minutes depending on input size and parameters
  • The application uses session-based file management for security