algo-naive-pattern-matching

name	algo-naive-pattern-matching
description	Brute-force O(n*m) sliding-window search for all overlapping matches of a pattern/motif/primer in text or DNA/protein strings, pure Python. Use for one-off exact search, or to benchmark the naive baseline before KMP/Rabin-Karp/Boyer-Moore.
tool_type	python
primary_tool	Python

Naive Pattern Matching

When to Use

• A quick, one-off exact substring search where preprocessing (building a prefix table, hash, or automaton) isn't worth it.
• Locating a short motif, primer, restriction site, or adapter in a DNA/protein string when the pattern is small relative to the text.
• Teaching/benchmarking context: establishing the O(n*m) baseline before introducing KMP, Rabin-Karp, or Boyer-Moore.
• Diagnosing why a hand-rolled substring scan is slow — e.g. it degrades toward O(n*m) on low-entropy text (poly-A runs, "AAAA...B"-style inputs, repetitive DNA).

Version Compatibility

Pure Python standard library only — no third-party dependencies. Works unchanged on Python >= 3.8; the list[int] return-type hint needs Python >= 3.9 or from __future__ import annotations on 3.8.

Prerequisites

• Comfortable with Python strings/lists and basic O-notation.
• No packages to install.
• Helpful next steps: algo-kmp-algorithm (linear-time exact match), algo-rabin-karp (rolling-hash alternative), algo-complexity-analysis (amortized analysis).

Algorithm

Slide the pattern over the text one position at a time; at each position compare character by character until a mismatch or a full match.

Goal: find every start index where pattern occurs in text, including overlapping occurrences, with no preprocessing. Approach: for each candidate start i in range(n - m + 1), compare text[i+j] to pattern[j] for j = 0..m-1; stop at the first mismatch (short-circuit) and record i on a full match. Never skip ahead on mismatch — that's exactly what KMP/Boyer-Moore improve on.

def naive_search(text: str, pattern: str) -> list[int]:
    """Find all (possibly overlapping) start indices of `pattern` in `text`.

    Time:  O(n) best/average case (mismatches found quickly), O(n * m) worst
           case (many partial matches, e.g. text="AAAA...AAB", pattern="AAAB").
    Space: O(1) auxiliary (O(k) for the result list with k matches).
    """
    n, m = len(text), len(pattern)
    positions: list[int] = []

    if m == 0:
        return list(range(n + 1))  # empty pattern matches everywhere
    if m > n:
        return []

    for i in range(n - m + 1):
        match = True
        for j in range(m):
            if text[i + j] != pattern[j]:
                match = False
                break  # short-circuit: this is what makes best-case O(n)
        if match:
            positions.append(i)
    return positions


def count_comparisons(text: str, pattern: str) -> int:
    """Count total character comparisons naive_search would perform.

    Useful for demonstrating best- vs worst-case behavior, e.g. on
    low-entropy DNA text: count_comparisons("AAAAAAAAAB", "AAAAB") is
    close to n * m, while a random/high-alphabet text is close to n.
    """
    n, m = len(text), len(pattern)
    total = 0
    for i in range(n - m + 1):
        for j in range(m):
            total += 1
            if text[i + j] != pattern[j]:
                break
    return total

Apply it directly to a DNA/protein sequence — the algorithm is alphabet-agnostic:

def find_motif(sequence: str, motif: str, case_sensitive: bool = False) -> list[int]:
    """Find all start positions of `motif` (e.g. a primer or restriction
    site) in a DNA/protein `sequence` using naive search.
    """
    if not case_sensitive:
        sequence, motif = sequence.upper(), motif.upper()
    return naive_search(sequence, motif)

Example: find_motif("ATGCGATCGATCGATAAG", "GATC") returns [4, 8] — overlapping matches are kept.

Complexity

Case	Time	When
Best	O(n)	First character mismatches quickly (large alphabet, low repetition)
Worst	O(n * m)	Many partial matches, e.g. text="AAAA...AAB", pattern="AAAB"
Average	O(n) for large alphabets	Random text, mismatches found in ~1-2 comparisons per position
Space	O(1) auxiliary	O(k) for storing k match positions

When Naive Is Fine

• Small patterns: m is small relative to n (e.g. a short primer in a document), so O(n*m) ~ O(n).
• Large alphabet: more distinct characters means mismatches are found within the first 1-2 comparisons on average.
• One-off search: no preprocessing to amortize (contrast with KMP's O(m) prefix table or Boyer-Moore's shift tables).
• Few expected occurrences: if the pattern rarely matches, most attempts fail on the first character.

Why It's Inefficient (and What Fixes It)

After a partial match fails, naive search discards everything it learned and restarts from scratch at the next position — it never uses the fact that, say, text[i+1:i+5] was already confirmed to equal pattern[0:4].

Algorithm	Time	Key Idea
KMP	O(n + m)	Prefix/failure function skips already-verified characters after a mismatch
Rabin-Karp	O(n + m) avg	Rolling hash gives O(1) amortized window comparison
Boyer-Moore	O(n/m) best	Bad-character/good-suffix rules skip large chunks of text

Pitfalls

• Finds overlapping matches by default (e.g. naive_search("ABABABA", "ABA") -> [0, 2, 4]) — this is correct, expected behavior, not a bug to "fix".
• Python's built-in str.find() / in use a highly optimized mix of Boyer-Moore-Horspool internally and will outperform a hand-written naive loop — don't hand-roll this for production code; use it only when you need custom match logic (e.g. mismatch tolerance) or are teaching the baseline.
• Worst case is triggered by low-entropy text — small alphabets like DNA's "ACGT" or poly-A/poly-T runs cause far more partial matches than English text or protein's 20-letter alphabet.
• m > n and m == 0 are easy to mishandle — always short-circuit both before the main loop (empty pattern conventionally matches at every position, including n).

See Also

• algo-kmp-algorithm — O(n + m) exact match via prefix function; the algorithm this baseline motivates.
• algo-rabin-karp — rolling-hash alternative, good for multiple-pattern search.
• algo-dfa-matching — precomputed state machine, O(n) search with zero backtracking.
• algo-aho-corasick — searches many patterns simultaneously in one linear pass.