Lecture 26: Sequence Alignment and Shortest Paths

$ \def\opt{ {\mathrm{opt}} } $

COSC 311 Algorithms, Fall 2022


  1. Sequence Alignment
  2. Shortest Paths, Revisited

Matching Between Strings

Given strings $X$ and $Y$ form a matching between characters

  • matching $M$ is a set of pairs of matched indices

Rules for matching:

  • each character is matched with at most one other character
    • some characters may be unmatched
  • matched characters cannot “cross”
    • if $(i, j)$, $(i’, j’)$ are matched with $i < i’$, then $j < j’$

Sequence Alignment Problem


  • Sequences $X$ and $Y$ of characters of length $n$ and $m$, respectively
  • Penalties $\delta, \alpha$ for omission/mismatch


  • A matching $M$ between indices of $X$ and $Y$
  • $M$ minimizes total penalty of matching

An Observation


  • $X$ sequence of length $n$
  • $Y$ sequence of length $m$
  • $M$ a matching between $[1, n]$ and $[1, m]$

Claim. Then at least one of the following holds:

  1. $(n, m)$ is in $M$
  2. $n$ is unmatched in $M$
  3. $m$ is unmatched in $M$


A Recursive Solution?

Idea. Use previous claim to give recursive characterization of optimal alignment.



  • $\opt(i, j) = $ minimum penalty of aligning $X[1..i]$ and $Y[1..j]$
  • $M_{i,j}$ is minimum penalty matching between $X[1..i]$ and $Y[1..j]$
  • by claim, there are three cases
    1. $(i, j) \in M_{i, j}$
    2. $i$ unmatched in $M_{i, j}$
    3. $j$ unmatched in $M_{i, j}$

Recursive Solution?

Question. What is a recurrence relation for $\opt(i, j)$?

Iterative Solution

Construct a two dimensional array p[0..n, 0..m]

  • p[i, j] should store $\opt(i, j)$

Question 1. How to initialize p?

Question 2. How to fill out p?


  • $X = [R, I, T, E]$
  • $Y = [T, I, E, R]$
  • $\delta = \alpha = 1$

Algorithm Pseudocode

  Alignment(X, Y, a, d):
    p <- 2d array of dimension (n+1) x (m+1)
    for i from 0 to n, p[i, 0] <- i * d
    for j from 0 to m, p[0, j] <- j * d
    for i from 1 to n
      for j from 1 to m
        unmatchX <- p[i-1, j] + d
        unmatchY <- p[i,j-1] + d
        match <- p[i-1,j-1]
        if X[i] != Y[j] then match <- match + a
        p[i, j] <- Min(unmatchX, unmatchY, match)
    return p[n, m]

Running time?


Optimal alignment between strings can be found in $O(n m)$ time where strings have lengths $n$ and $m$, respectively.

Shortest Paths, Revisited

Directed Graphs and Paths

Representing Directed Graphs

Adjacency List

  • $v$’s neighbors are outgoing neighbors


Single Source Shortest Paths (SSSP):


  • (Directed) graph $G = (V, E)$, edge weights $w$
  • Starting vertex $u$


  • $d(v) = $ distance from $u$ to $v$ for every vertex $v$

Previous Algorithms

  1. Breadth-first Search (BFS)
    • solves SSSP when all edge weights are $1$
  2. Dijkstra’s Algorithm
    • solves SSSP when all edge weights are $\geq 0$

Question. What if edge weights can be negative?

Negative Dijkstra


Assume. $G$ does not contain any negative weight cycles.



Claim. $G$ a graph with $n$ vertices, $u, v$ vertices in $G$. If $G$ does not contain negative weight cycles, then the shortest (weighted) path from $u$ to $v$ contains at most $n-1$ edges.



Suppose shortest path from $u$ to $x$ contains $j$ hops.

  • $v$ is $x$’s “parent” along path
  • $d(u, x) = d(u, v) + w(v, x)$
  • shortest path from $u$ to $v$ has $j-1$ hops

Dynamic Programming Approach

Idea. For each vertex $v$ and each $j = 1, 2, \ldots, n-1$ compute $d_j(u, v) = $ length of shortest path from $u$ to $v$ with at most $j$ hops.

  • Note $d(u, v) = d_{n-1}(u, v)$.


Question 1. How to initialize $d_0(u, v)$?

Question 2. Given $d_j(u, v)$ for all v, how to find $d_{j+1}(u, v)$?


Bellman-Ford Algorithm

  Bellman-Ford(V, E, w, u)
    d <- 2d array [0..n-1, 1..n]
    for v = 1 to n do d[0, v] <- infinity
    d[0, u] <- 0
    for j = 1 to n-1 do
      for each vertex v in V set d[j, v] <- d[j-1,v]
      for each vertex v in V
        for each neighbor x of v
          d[j, x] <- Min(d[j, x], d[j-1, v] + w[v, x])
    return d[n-1]

Running time?

Dijkstra vs Bellman-Ford?

Next Time

Network Flow!