MotifFinding – Mini-Project (Bioinformatics Practice)

This mini-project implements a simple motif search tool in Python, as part of my bioinformatics learning roadmap.
The goal is to practice working with DNA strings, file input/output, and clean, readable code that could fit into a basic bioinformatics pipeline. Duration : 1 full day 11/16/2025

1. Project structure

MotifFinding/
    data/
        sequence.txt        # Input DNA sequence
        motif.txt           # Input motif/pattern to search for
    outputs/
        motif_positions.txt # Output: 1-based positions of the motif in the sequence
    src_perso/
        motif_finding.py    # Main script with functions and examples
    README.md

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2. Core idea

Given:

• a DNA sequence (for example: GATATATGCATATACTT)
• a motif/pattern (for example: ATAT)

the script finds all 1-based starting positions where the motif appears in the sequence and writes them into a text file.

Example output:

2 4 10

This corresponds to the classical “Finding a Motif in DNA” exercise, widely used in introductory bioinformatics training.

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3. Implementation details

All the core logic is in src_perso/motif_finding.py and is organized in three main functions:

• find_motif(sequence: str, pattern: str) -> list[int]

  • Cleans the inputs (removes spaces/newlines, converts to uppercase)
  • Slides a window across the sequence
  • Returns all 1-based positions where the motif matches

• load_from_files(seq_path: str, motif_path: str) -> tuple[str, str]

  • Reads a DNA sequence and a motif from two text files
  • Returns both as raw strings

• save_positions(positions: list[int], out_path: str)

  • Saves the list of positions into a text file
  • If there are no matches, writes: No occurrences found.

The if __name__ == "__main__": block contains:

• Example 1: simple in-memory example with hard-coded strings
• Example 2: realistic use case using data/ → outputs/

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4. How to run the project

From the src_perso directory:

cd src_perso
python motif_finding.py

You should see in the terminal:

• Example 1: direct test with sequence and motif
• Example 2: results loaded from the files in data/

The positions will be saved automatically in:

../outputs/motif_positions.txt

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5. Example input files

data/sequence.txt

GATATATGCATATACTT

data/motif.txt

ATAT

This produces the following output:

2 4 10

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6. Requirements

• Python 3.8+
• No external libraries required

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7. Learning notes

This mini-project is part of a bioinformatics learning track where I practice:

• DNA string manipulation in Python
• Reading and writing text files
• Building clean and well-documented functions
• Organizing mini-projects for GitHub (folders, scripts, README)

Possible extensions include:

• FASTA file handling
• Using Biopython
• Searching motifs in larger genomes
• Scanning for multiple motifs