mirnaprotpred 0.1.5

A package for miRNA protein prediction with SeqFinder and validator modules

miRNAProtPred

A Python package for miRNA protein prediction with SeqFinder and validator modules.

Overview

miRNAProtPred is a bioinformatics tool designed to identify miRNA target sequences in DNA, RNA, or protein sequences. It uses the Boyer-Moore string matching algorithm combined with BLAST and ViennaRNA for comprehensive miRNA target prediction and validation.

Features

• SeqFinder: Find miRNA target sequences in DNA, RNA, or protein sequences

  • Automatic sequence type detection (DNA/RNA/Protein)
  • BLAST integration for protein sequence analysis
  • Boyer-Moore pattern matching for efficient sequence searching
  • ViennaRNA integration for minimum free energy (MFE) calculation
  • Probability scoring (High/Medium/Low) based on MFE values
  • Results export to CSV format

• Validator: Validate miRNA-mRNA interactions (experimental module)

Installation

Prerequisites

• Python >= 3.7
• Required Python packages:
  • pandas >= 1.3.0
  • openpyxl >= 3.0.0
  • biopython
  • ViennaRNA
  • pyfiglet

Install from source

git clone https://github.com/somenath-combio/mirnaprotpred.git
cd mirnaprotpred
pip install -e .

Usage

SeqFinder

Find miRNA target sequences in your input sequence:

SeqFinder <sequence>

Examples:

# DNA sequence
SeqFinder "ATGCATGCATGCATGC"

# RNA sequence
SeqFinder "AUGCAUGCAUGCAUGC"

# Protein sequence
SeqFinder "MKKLAVSLLLFLSSLA"

The tool will:

1. Automatically detect the sequence type
2. Search for miRNA seed sequences from the database
3. Calculate minimum free energy (MFE) using ViennaRNA
4. Assign probability scores (High: MFE ≤ -15, Medium: -15 < MFE ≤ -10, Low: MFE > -10)
5. Display results sorted by MFE
6. Optionally save results to CSV

Validator

Validate miRNA-mRNA interactions:

validator <miRNA_sequence> <mRNA_sequence>

Example:

validator "AUGCAUGC" "GCAUGCAU"

Data Requirements

The SeqFinder module requires a data file located at data/data.xlsx containing:

• miRNA descriptions
• Human miRNA IDs
• Accession numbers
• Sequences
• Seed sequences (seed1, seed2, seed3 columns)

Output

SeqFinder generates results with the following columns:

• Description: miRNA description
• Human miRNA ID: Identifier for the miRNA
• Accession: Accession number
• Sequence: Full miRNA sequence
• Seed: Matched seed sequence
• Position: Position of the match in the input sequence
• CTS: Complementary target site sequence
• MFE: Minimum free energy
• Prob: Probability score (High/Medium/Low)

How It Works

1. Sequence Type Detection: Automatically identifies whether the input is DNA, RNA, or protein
2. Protein Processing: For protein sequences, uses BLAST to retrieve the corresponding nucleotide sequence
3. Pattern Matching: Uses the Boyer-Moore algorithm to find miRNA seed sequences
4. Energy Calculation: Calculates duplex formation energy using ViennaRNA
5. Scoring: Assigns probability based on MFE thresholds

License

MIT License

Author

Sudipta Sardar ([e-mail])

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

Citation

If you use this tool in your research, please cite appropriately.