pattern-searching 0.1.3

Single-pattern and multiple-pattern string searching algorithms in Python

Pattern Searching Algorithms

This package provides single-pattern and multiple-pattern string searching algorithms in Python.
It is useful for students, programmers, and bioinformatics enthusiasts to learn, practice, and experiment with text and DNA/protein sequence analysis.

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🎯 Relevance to Bioinformatics

Pattern searching is crucial for:

• Finding motifs in DNA sequences (e.g., promoters, binding sites)
• Identifying repeated sequences or mutations in genomes
• Searching multiple motifs efficiently in large genomic datasets

These algorithms are foundational for sequence analysis, text processing, and bioinformatics data mining.

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🧩 Single-Pattern Algorithms (Recherche d’un seul motif)

Algorithm	Description
Naive	Simple brute-force search for a single pattern.
Morris-Pratt	Optimized for repeated patterns using prefix preprocessing.
Boyer-Moore	Skips unmatched characters using bad character heuristic.
Rabin-Karp	Uses hashing for pattern search.

Example:

from algorithms.single_pattern.naive import naive_search

text = "ABABDABACDABABCABAB"
pattern = "ABABCABAB"
naive_search(text, pattern)

🧩 Multiple-Pattern Algorithms (Recherche de plusieurs motifs)

Algorithm	Description
Rabin-Karp (Multiple)	Hash-based search for multiple patterns at once.
Aho-Corasick	Builds a finite automaton for all patterns; very efficient.
Wu-Manber	Optimized multiple-pattern search using block shifts.
Commentz-Walter	Combines Boyer-Moore logic with multiple-pattern optimization.

Example:

from algorithms.multiple_pattern.aho_corasick import AhoCorasick

text = "ACGTACGTGACG"
patterns = ["ACG", "GAC"]
ac = AhoCorasick(patterns)
ac.search(text)

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🚀 Usage

Clone the repository:

git clone https://github.com/HADIL19/Pattern-Searching.git
cd Pattern-Searching

Install the package locally:

pip install -e .

Run any algorithm:

python algorithms/single_pattern/naive.py
python algorithms/multiple_pattern/aho_corasick.py

📚 Resources

Check resources/pattern_searching_links.md for tutorials and detailed explanations:

• Pattern Searching on GeeksforGeeks
• KMP, Rabin-Karp, Boyer-Moore, Aho-Corasick tutorials
• Wu-Manber and Commentz-Walter references

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⚖️ License

This project is licensed under the MIT License.
See the LICENSE file for full details.

You are free to **use, copy, modify, merge, publish, distribute, subl