algo-kmp-algorithm

name	algo-kmp-algorithm
description	Find all overlapping exact occurrences of a pattern/motif/primer in a string or DNA sequence in O(n+m) time via KMP's prefix/failure-function. Use for exact substring search, motif/primer location, or a slow naive O(n*m) scan.
tool_type	python
primary_tool	Python

Knuth-Morris-Pratt (KMP) Algorithm

When to Use

• Finding all occurrences (including overlapping ones) of a short pattern in a long text/sequence in linear time.
• Locating a motif, primer, adapter, or restriction site inside a DNA/protein string without allowing mismatches.
• Any place a naive O(n*m) substring scan is a bottleneck (large genome/text, many matches).
• Building blocks for multi-pattern search (see Aho-Corasick) or as a subroutine in string algorithms courses/interviews.

Version Compatibility

Pure Python standard library only — no third-party dependencies. Works unchanged on Python >= 3.8 (uses only list/str built-ins; type hints like list[int] need Python >= 3.9 or from __future__ import annotations).

Prerequisites

• Comfortable with Python strings/lists and O-notation.
• No packages to install.
• Helpful prior context: algo-naive-pattern-matching (the baseline this improves on), algo-complexity-analysis (amortized analysis).

Key Insight

After a partial match fails, the prefix function tells us how far to shift the pattern without re-comparing characters we already know match. The text pointer i never moves backward — only the pattern pointer j falls back.

Prefix Function (Failure Function)

pi[i] = length of the longest proper prefix of P[0..i] that is also a suffix of P[0..i].

Example: Pattern "ABABACA" -> pi = [0, 0, 1, 2, 3, 0, 1]

Goal: build the prefix table in O(n) so KMP search never re-scans matched characters. Approach: track j, the length of the current longest prefix-suffix match; on a mismatch, fall back using previously computed pi values instead of restarting from 0.

def build_prefix(pattern: str) -> list[int]:
    """Build the KMP prefix (failure) function for `pattern`.

    pi[i] = length of the longest proper prefix of pattern[0..i]
    that is also a suffix of pattern[0..i].

    Time: O(n) amortized (j increases at most n times total, so it
    can decrease at most n times total across the whole loop).
    Space: O(n).
    """
    n = len(pattern)
    if n == 0:
        return []
    pi = [0] * n
    j = 0  # length of previous longest prefix-suffix
    for i in range(1, n):
        while j > 0 and pattern[j] != pattern[i]:
            j = pi[j - 1]
        if pattern[j] == pattern[i]:
            j += 1
        pi[i] = j
    return pi

KMP Search — O(n + m)

Goal: find every start index where pattern occurs in text, including overlapping occurrences. Approach: slide pattern against text using the prefix table to skip already-verified characters after a mismatch; on a full match, fall back to pi[j-1] to keep looking for the next (possibly overlapping) hit instead of restarting at j = 0.

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

    Time: O(n + m) where n = len(text), m = len(pattern).
    Space: O(m) for the prefix table.
    """
    if not pattern or len(pattern) > len(text):
        return []
    pi = build_prefix(pattern)
    matches = []
    j = 0  # number of matched pattern characters so far
    for i in range(len(text)):
        while j > 0 and text[i] != pattern[j]:
            j = pi[j - 1]
        if text[i] == pattern[j]:
            j += 1
        if j == len(pattern):
            matches.append(i - j + 1)
            j = pi[j - 1]  # keep scanning for overlapping matches
    return matches


def find_motif_in_sequence(sequence: str, motif: str) -> list[int]:
    """Convenience wrapper for DNA/protein motif search (e.g. a primer or
    restriction site) using KMP. Sequence and motif are matched literally
    (uppercase both first if case should be ignored).
    """
    return kmp_search(sequence, motif)

Complexity

	Time	Space
Preprocessing (prefix table)	O(m)	O(m)
Search	O(n)	O(1) extra
Total	O(n + m)	O(m)

Pitfalls

• The prefix-table build looks O(n^2) due to the nested while inside the for, but the amortized argument (j can only decrease as many times as it increased) guarantees O(n).
• KMP finds overlapping matches by default — j = pi[j - 1] after a full match continues searching instead of resetting j = 0.
• KMP does exact matching only; it does not tolerate mismatches/indels — for approximate/fuzzy matching use edit-distance or seed-and-extend approaches instead.
• For searching many patterns at once, running kmp_search per pattern is O(k*(n+m)); use Aho-Corasick to search all patterns in one O(n + sum(m) + matches) pass.
• Empty pattern or pattern longer than text must short-circuit to [] — both are handled above, but easy to forget in a from-scratch reimplementation.

See Also

• algo-naive-pattern-matching — the O(n*m) baseline KMP improves on.
• algo-rabin-karp — hashing-based alternative, good for multiple-pattern rolling-hash search.
• algo-aho-corasick — generalizes KMP's failure function to search many patterns simultaneously.
• algo-dfa-matching — builds a full state machine instead of a fallback table; O(n) search with no backtracking logic.