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Example Datasets

BioRemPP provides ready-to-use example datasets to help you get started quickly. These datasets demonstrate proper input formatting and represent biologically relevant organisms used in bioremediation research.

Quick Access

Download example dataset:

  • From homepage: use Need a KO Input Example? -> Download Example
  • Load directly: click Use Example Data in the upload panel (no download required)

Example Dataset: Minimal Demo

Overview

  • Samples: 2
  • KO identifiers: 10 total (5 per sample)
  • Purpose: Demonstrate proper input format and quick testing

Dataset Content

>Sample1
K00031
K00032
K00090
K00042
K00052
>Sample2
K00031
K00032
K00090
K00042
K00052

What This Demonstrates

  • Proper sample headers: Each sample starts with > followed by name
  • Valid KO format: All identifiers are K + 5 digits
  • No blank lines: Samples immediately follow KO lists
  • Shared KOs: Both samples have identical KO profiles (useful for testing comparative analyses)

For complete format specification, see Input Format.

Published Demonstration Dataset: Nine Representative Organisms

Overview

BioRemPP's published demonstration uses nine representative organisms spanning three principal groups in bioremediation:

  • Total samples: 9 (3 bacteria, 3 fungi, 3 microalgae/cyanobacteria)
  • Purpose: Demonstrate multi-kingdom comparative analysis
  • Based on: Organisms relevant to hydrocarbon bioremediation studies

Organisms Included

Bacteria

Organism KEGG Code Notes
Acinetobacter baumannii acb Gram-negative, opportunistic pathogen with xenobiotic degradation capacity
Enterobacter asburiae eau Emerging bioremediation agent, aromatic compound degradation
Pseudomonas aeruginosa pae Model organism for biodegradation, versatile metabolic capacity

Fungi

Organism KEGG Code Notes
Aspergillus nidulans ani Filamentous fungus, lignocellulose degradation
Fusarium graminearum fgr Plant pathogen, aromatic compound transformation
Cryptococcus gattii cgi Yeast, environmental stress tolerance

Microalgae / Cyanobacteria

Organism KEGG Code Notes
Chlorella variabilis cvr Green microalga, heavy metal biosorption
Nannochloropsis gaditana ngd Marine microalga, lipid accumulation
Synechocystis sp. syn Model cyanobacterium, photosynthetic bioremediation

Scientific Reference

These organisms were selected based on their relevance in hydrocarbon bioremediation studies:

Publication:
Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era
Microorganisms 2021, 9, 1695.
DOI: 10.3390/microorganisms9081695

How to Use This Dataset

If you have genome annotations for these organisms:

  1. Annotate genomes using KAAS, eggNOG-mapper, or similar tools
  2. Extract KO identifiers for each organism
  3. Format as described in Input Format
  4. Compare with BioRemPP Database to assess bioremediation potential

Typical analyses:

  • Cross-kingdom comparison: Compare bacterial vs. fungal vs. microalgal bioremediation potential
  • Consortium optimization: Identify complementary gene profiles for mixed-culture applications
  • Regulatory compliance: Verify presence of genes for priority pollutant degradation

See Use Cases Index for all 56 analytical workflows available for these types of comparisons.

Creating Your Own Dataset

Step 1: Choose Your Samples

Sample selection criteria:

  • Biological relevance: Organisms or communities with suspected bioremediation capacity
  • Genome availability: Complete or draft genomes annotated with KO identifiers
  • Comparative context: Include replicates or related samples for comparative analysis

Step 2: Annotate Genomes with KO Identifiers

Tool Input Output URL
KAAS Nucleotide sequences (FASTA) KO assignments https://www.genome.jp/kaas-bin/kaas_main
eggNOG-mapper Protein/nucleotide sequences KO + COG + GO http://eggnog-mapper.embl.de/
DIAMOND Protein sequences + KEGG DB BLAST-style hits → KO https://github.com/bbuchfink/diamond
GhostKOALA Nucleotide sequences KO assignments https://www.kegg.jp/ghostkoala/

Step 3: Format for BioRemPP

Format KO assignments as:

>YourSampleName
K00001
K00002
K00003
...
>YourSampleName2
K00010
K00020
K00030
...

Important formatting rules:

  • Sample names: No spaces (use underscores or hyphens)
  • KO format: Exactly K + 5 digits (remove ko: prefix if present)
  • No duplicates: Each KO should appear once per sample
  • No blank lines: Samples follow immediately after KO lists

Step 4: Validate Format

Before uploading:

  • Check for blank lines (remove all)
  • Verify sample headers start with >
  • Confirm all KOs match K##### format
  • Ensure file is UTF-8 encoded

Quick validation:

# Count samples (should match expected)
grep -c "^>" your_dataset.txt

# Count total KOs
grep -c "^K" your_dataset.txt

# Check for invalid lines (should return nothing)
grep -v "^>" your_dataset.txt | grep -v "^K"

Dataset Quality Checklist

Before uploading, verify:

  • All sample headers start with >
  • All sample names contain no spaces
  • All KO identifiers are exactly K##### format
  • No blank lines between samples
  • File is UTF-8 encoded (not UTF-16 or Latin-1)
  • File size <5 MB
  • Total samples ≤100
  • Total KO identifiers ≤500,000

Troubleshooting Example Datasets

"Example data doesn't load"

Possible causes:

  • Browser cache issue
  • Server connectivity problem

Solutions:

  1. Refresh browser (Ctrl+F5 or Cmd+Shift+R)
  2. Clear browser cache
  3. Try different browser (Chrome, Firefox, Safari)
  4. Download example file manually and upload