Bioinformatics algorithms and data structures
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Bioinformatics Algorithms and Data Structures. Chapter 11: Core String Edits Lecturer: Dr. Rose Slides by: Dr. Rose January 30 & February 1, 2007. Core String Edits. This chapter introduces inexact matching Inexact matching is used to compute similarity.

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Bioinformatics algorithms and data structures

Bioinformatics Algorithms and Data Structures

Chapter 11: Core String Edits

Lecturer: Dr. Rose

Slides by: Dr. Rose

January 30 & February 1, 2007


Core string edits

Core String Edits

  • This chapter introduces inexact matching

    • Inexact matching is used to compute similarity.

    • Sequences similarity is a key concept.

    • Sequence similarity implies

      • Structural similarity

      • Functional similarity

    • We will consider a dynamic programming approach to inexact matching.


Edit distance

Edit Distance

  • One measure of similarity between two strings is their edit distance.

  • This is a measure of the number of operations required to transform the first string into the other.

  • Single character operations:

    • Deletion of a character in the first string

    • Insertion of a character in the first string

    • Substitution of a character from the second character into the second string

    • Match a character in the first string with a character of the second.


Edit distance1

Edit Distance

Example from textbook: transform vintner to writers

vintner replace v with w wintner

wintner insert r after w wrintner

wrintner match i  wrintner

wrintner delete n writner

writnermatch t writner

writnerdelete n writer

writermatch e writer

writermatch r writer

writerinsert s writers


Edit distance2

Edit Distance

Let S = {I, D, R, M} be the edit alphabet

Defn. An edit transcript of two strings is a string over S describing a transformation of one string into another.

Defn. The edit distance between two strings is defined as the minimum number of edit operations needed to transform the first into the second. Matches are not included in the count.

Edit distance is also called Levenshtein distance.


Edit distance3

Edit Distance

Defn. An optimal transcript is an edit transcript with the minimal number of edit operations for transforming one string into another.

Note: optimal transcripts may not be unique.

Defn. The edit distance problem entails computing the edit distance between two strings along with an optimal transcript.


String alignment

String Alignment

Defn. A global alignment of strings S1 and S2 is obtained by:

  • Inserting dashes/spaces into or at the ends of S1 and S2.

  • Aligning the two strings s.t. each character/space in either string is opposite a unique character/space in the other string.

    Example 1: S1 = qacdbd S2 = qawxb

    q a c - d b d

    q a w x - b -


String alignment1

String Alignment

Example 2: S1 = vintner S2 = writers

v - i n t n e r -

w r i - t - e r s

  • Mathematically, string alignment and edit transcripts are equivalent.

  • From a modeling perspective they are not equivalent.

  • Edit transcripts express the idea of mutational changes.


Dynamic programming

Dynamic Programming

  • Observation 1: There are many possible ways to transform one string into another.

  • Observation 2: This is like the knapsack problem

  • Recall: dynamic programming is used to solve knapsack-like problems.

  • Defn. Let D(i,j) denote the edit distance of S1[1..i] and S2[1..j].

    • That is, D(i,j) is the minimum number of edit ops needed to transform the first i characters of S1 into the first j characters of S2.


Dynamic programming1

Dynamic Programming

  • Notice that we can solve D(i,j) for all combination of lengths of prefixes of S1 and S2.

  • Examples: D(0,0),.., D(0,j), D(1,0),..,D(1,j), … D(i,j)

  • Dynamic programming is a divide and conquer method.

  • The three parts to dynamic programming are:

    • The recurrence relation

    • Tabular computation

    • Traceback


Dynamic programming2

Dynamic Programming

  • The recurrence relation expresses the recursive relation between a problem and smaller instances of the problem.

  • For any recursive relation, the base condition(s) must be specified.

  • Base conditions for D(i,j) are:

    • D(i,0) = i

      Q: Why is this true? What does it mean in terms of edit ops?

    • D(0,j) = j

      Q: Why is this true? What does it mean in terms of edit ops?


Dynamic programming3

Dynamic Programming

  • The general recurrence is given by:

    D(i,j) = min[D(i - 1, j) + 1, D(i, j - 1) + 1, D(i - 1, j - 1) + t (i,j) ]

    Here t (i,j) = 1 if S1(i) S2(j), o/w t (i,j) = 0.

  • Proof of correctness on Pages 218-219

  • Basic argument: D(i,j) must be one of :

    • D(i - 1, j) + 1

    • D(i, j - 1) + 1

    • D(i - 1, j - 1) + t (i,j)

      There are NO other ways of creating S2[1..j] from S1[1..i].


Dynamic programming4

Dynamic Programming

Q: How do we use the recurrence relation to efficiently compute D(i,j) ?

Wrong Answer: simply use recursion.

Q: Why is this the wrong answer?

A: recursion results in inefficient duplication of computations for subproblems.

Q: How much duplication?

A: Exponential duplication!

Example: Fibonacci numbers


Dynamic programming5

Dynamic Programming

Example: Fibonacci numbers

f(n) = f(n - 1) + f(n - 2)

Base conditions: f(0) = 0, f(1) = 1


Dynamic programming6

Dynamic Programming

  • Note: In calculating D(n,m), there are only (n + 1)  (m + 1) unique combinations of i and j.

  • Clearly an exponential number of computations is NOT required.

  • Soln: instead of going top-down with recursion, go bottom-up. Compute each combination only once.

    • Decide on a data structure to hold intermediate results.

    • Start from base conditions. These are the smallest D(i,j) values and are already defined.

    • Compute D(i,j) for larger values of i and j.


Dynamic programming7

Dynamic Programming

  • Example: Fibonacci numbers

  • Decide on a data structure: simple array

  • Start from base conditions: f(0) = 0, f(1) = 1

  • Compute f(i) for larger values of i. From bottom up.

  • Each f(i) is computed only once!


Dynamic programming8

Dynamic Programming

  • Q: What kind of data structure should we use for edit distance?

    • Has to be a random access data structure.

    • Has to support the dimensionality of the problem.

  • D(i,j) is two-dimensional: S1 and S2.

  • We will use a two-dimensional array, i.e., a table.


Dynamic programming9

Dynamic Programming

Example: edit distance from vintner to writers.

Fill in the base condition values.


Dynamic programming10

Dynamic Programming

  • Q: How do we fill in the other values?

  • A: use the recurrence:

    D(i,j) = min[D(i - 1, j) + 1, D(i, j - 1) + 1, D(i - 1, j - 1) + t (i,j) ]

    where t (i,j) = 1 if S1(i) S2(j), o/w t (i,j) = 0.

  • We can first compute D(1,1) because we have D(0,0), D(0,1), and D(1,0)

    • D(1,1) = min[ 1+1, 1+1, 0+1] = 1

  • Then we have all the values needed to compute in turn D(1,2), D(1,3),..,D(1,m)


Dynamic programming11

Dynamic Programming

First compute D(1,1) because we have D(0,0), D(0,1), and D(1,0)

Then compute in turn D(1,2), D(1,3),..,D(1,m)


Dynamic programming12

Dynamic Programming

Fill in subsequent values, row by row, from left to right.


Dynamic programming13

Dynamic Programming

Alternatively, first compute D(1,1) from D(0,0), D(0,1), and D(1,0)

Then compute in turn D(2,1), D(3,1),..,D(n,1)


Dynamic programming14

Dynamic Programming

Fill in subsequent values, column by column, from top to bottom.


Dynamic programming15

Dynamic Programming

  • Filling each cell entails a constant number of operations.

    • Cell (i,j) depends only on characters S1(i) and S2(j) and cells (i - 1, j - 1), (i, j - 1), and (i - 1, j).

  • There are O(nm) cells in the table

  • Consequently, we can compute the edit distance D(n, m) in O(nm) time by computing the table in O(nm).


Dynamic programming16

Dynamic Programming

  • Having computed the table we know the value of the optimal edit transcript.

  • Q: How do we extract the optimal edit transcript from the table?

  • A: One way would be to establish pointers from each cell, to predecessor cell(s) from which its value was derived, i.e,

    • If D(i,j) = D(i - 1, j) + 1 add a pointer from (i,j) to (i - 1, j)

    • If D(i,j) = D(i, j - 1) + 1add a pointer from (i,j) to (i, j - 1)

    • If D(i,j) = D(i - 1, j - 1) + t(i,j)add a pointer from (i,j) to (i - 1, j - 1)


Dynamic programming17

Dynamic Programming


Dynamic programming18

Dynamic Programming

  • We can recover an optimal edit sequence simply by following any path from (n,m) to (0,0)

  • The interpretation of the path links are:

    • A horizontal link , (i,j) (i,j-1), corresponds to an insertion of character S2(j) into S1.

    • A vertical link, (i,j) (i-1,j), corresponds to a deletion of S1(i) from S1.

    • A diagonal link, (i,j) (i-1,j-1), corresponds to a match S1(i) = S2(j) and a substitution if S1(i) S2(j)


Dynamic programming19

Dynamic Programming


Dynamic programming20

Dynamic Programming

An optimal edit path.

What edit transcript does

this path correspond to?

S,S,S,M,D,M,M,I


Dynamic programming21

Dynamic Programming

Another optimal edit path.

What edit transcript does

this path correspond to?

I,S,M,D,M,D,M,M,I


Dynamic programming22

Dynamic Programming

The third possible optimal edit

path. What edit transcript

does this path correspond to?

S,I,M,D,M,D,M,M,I


Dynamic programming23

Dynamic Programming

  • Alternatively we can interpret any path from (n,m) to (0,0) as an alignment of S1 and S2.

  • The interpretation of the path links are:

    • A horizontal link , (i,j) (i,j-1), corresponds to an insertion of a space/dash into S1.

    • A vertical link, (i,j) (i-1,j), corresponds to an insertion of a space/dash into S2.

    • A diagonal link, (i,j) (i-1,j-1), corresponds to a match if S1(i) = S2(j) or a mismatch if S1(i) S2(j)


Dynamic programming24

Dynamic Programming

Possible optimal path.

What alignment does this

optimal path correspond to?

w r i t - e r s

v i n t n e r -


Dynamic programming25

Dynamic Programming

A second possible optimal path.

What alignment does this

optimal path correspond to?

w r i - t - e r s

v - i n t n e r -


Dynamic programming26

Dynamic Programming

A third possible optimal path.

What alignment does this

optimal path correspond to?

w r i - t - e r s

- v i n t n e r -


Summary

Summary

  • Any path from (n,m) to (0,0) corresponds to an optimal edit sequence and an optimal alignment

  • We can recover all optimal edit sequences and alignments simply by extracting all paths from (n,m) to (0,0)

  • The correspondence between paths and edit sequences is one-to-one.

  • The correspondence between paths and alignments is one-to-one.


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