The Needleman-Wunsch algorithm for

sequence alignment
7th Melbourne Bioinformatics Course
Vladimir Likić, Ph.D.
e-mail: [email protected]

Bio21 Molecular Science and Biotechnology Institute

The University of Melbourne

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Outline of the talk

Sequence comparison and sequence alignment.

Types of sequence alignment.

The scoring scheme, substitution matrices, gaps.

The Needleman-Wunsch algorithm for global sequence

alignment.

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Sequence comparison

To observe patterns of conservation (or variability).

To find the common motifs present in both sequences.

To assess whether it is likely that two sequences evolved

from the same sequence.

To find out which sequences from the database are similar

to the sequence at hand.

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Two routes for sequence comparison

dotplot – visual, qualitative

sequence alignment – exact and quantitative. Involves:

1. Construction of the best alignment between the
sequences.
2. Assessment of the similarity from the alignment.

There are three different types of sequence alignment:

Global alignment
Local alignment
Multiple sequence alignment

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Global sequence alignment

The best alignment over the entire length of two

sequences

Suitable when the two sequences are of similar length,

with a significant degree of similarity throughout.

Example:
SIMILARITY
PI-LLAR---

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Local sequence alignment

Involving stretches that are shorter than the entire

sequences, possibly more than one.

Suitable when comparing substantially different sequences,

which possibly differ significantly in length, and have only
a short patches of similarity.

For example, the local alignment of SIMILARITY and

PILLAR:
MILAR
ILLAR

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Multiple sequence alignment

Simultaneous alignment of more than two sequences.

Suitable when searching for subtle conserved sequence

patterns in a protein family, and when more than two
sequences of the protein family are available.

For example:
SIMILARITY
PI-LLAR---
--MOLARITY

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Alignment ”by eye”

Consider the ”best” alignment of ATGGCGT and ATGAGT

ATGGCGT
*** !**
ATG-AGT

Intuitively we seek an alignment to maximize the number

of residue-to-residue matches.

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A mathematical framework

Sequence alignment is the establishment of

residue-to-residue correspondence between two or more
sequences such that the order of residues in each sequence
is preserved.

A gap, which indicates a residue-to-nothing match, may

be introduced in either sequence.

A gap-to-gap match is meaningless and is not allowed.

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The scoring scheme

Give two sequences we need a number to associate with

each possible alignment (i.e. the alignment score =
goodness of alignment).

The scoring scheme is a set of rules which assigns the

alignment score to any given alignment of two sequences.
1. The scoring scheme is residue based: it consists of residue
substitution scores (i.e. score for each possible residue
alignment), plus penalties for gaps.
2. The alignment score is the sum of substitution scores and
gap penalties.

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A simple scoring scheme

Use +1 as a reward for a match, -1 as the penalty

for a mismatch, and ignore gaps

The best alignment ”by eye” from before:

ATGGCGT
ATG-AGT score: +1 + 1 + 1 + 0 − 1 + 1 + 1 = 4

An alternative alignment:

ATGGCGT
A-TGAGT score: +1 + 0 − 1 + 1 − 1 + 1 + 1 = 2

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The substitution matrix

A concise way to express the residue substitution costs can

be achieved with a N × N matrix (N is 4 for DNA and 20
for proteins).

The substitution matrix for the simple scoring scheme:

C T A G
C 1 -1 -1 -1
T -1 1 -1 -1
A -1 -1 1 -1
G -1 -1 -1 1

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A better substitution matrix

A, G are purines (pyrimidine ring fused to an imidazole

ring), T, C are pyrimidines (one six-membered ring).

Assume we believe that from evolutionary standpoint

purine/pyrimidine mutations are less likely to occur
compared to purine/purine (pyrimidine/pyrimidine)
mutations. Can we capture this in a substitution matrix?

C T A G
C 2 1 -1 -1
T 1 2 -1 -1
A -1 -1 2 1
G -1 -1 1 2
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Protein substitution matrices

Protein substitution matrices are significantly more

complex than DNA scoring matrices.

Proteins are composed of twenty amino acids, and

physico-chemical properties of individual amino acids vary
considerably.

A protein substitution matrix can be based on any property

of amino acids: size, polarity, charge, hydrophobicity.

In practice the most important are evolutionary

substitution matrices.

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Evolutionary substitution matrices

PAM (”point accepted mutation”) family

PAM250, PAM120, etc.

BLOSUM (”Blocks substitution matrix”) family

BLOSUM62, BLOSUM50, etc.

The substitution scores of both PAM and BLOSUM

matrices are derived from the analysis of known
alignments of closely related proteins.

The BLOSUM matrices are newer and considered better.

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BLOSUM62 substitution matrix

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Gaps

So far we ignored gaps (amounts to gap penalty of 0)

A gap corresponds to an insertion or a deletion of a

residue

A conventional wisdom dictates that the penalty for a gap

must be several times greater than the penalty for a
mutation. That is because a gap/extra residue
Interrupts the entire polymer chain
In DNA shifts the reading frame

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Gap initiation and extension

The conventional wisdom: the creation of a new gap

should be strongly disfavored.

However, once created insertions/deletions of chunks of

more than one residue should be much less expensive (i.e.
insertion of domains often occurs).

A simple yet effective solution is affine gap penalties:

γ(n) = −o − (n − 1)e

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Affine gaps: a physical insight

Affine gaps favor the alignment:

ATGTAGTGTATAGTACATGCA
ATGTAG-------TACATGCA
Over the alignment:
ATGTAGTGTATAGTACATGCA
ATGTA--G--TA---CATGCA

Exactly what we want from the biological viewpoint.

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The alignment score with BLOSUM62

Consider two alternative alignments of ANRGDFS and

ANREFS with the gap opening penalty of 10:
ANRGDFS
ANR-EFS score: 4 + 6 + 5 − 10 + 2 + 6 + 4 = 17
ANRGDFS
ANRE-FS score: 4 + 6 + 5 − 2 − 10 + 6 + 4 = 13

The scoring scheme provides us with the quantitative

measure of how good is some alignment relative to
alternative alignments. However the scoring scheme
does not tell us how to find the best alignment.

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How do we find the best alignment?

Brute-force approach:
Generate the list all possible alignments between two
sequences, score them
Select the alignment with the best score

The number of possible global alignments between two

sequences of length N is

22N
√
πN

For two sequences of 250 residues this is ∼ 10149

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The Needleman-Wunsch algorithm

A smart way to reduce the massive number of possibilities

that need to be considered, yet still guarantees that the
best solution will be found (Saul Needleman and Christian
Wunsch, 1970).

The basic idea is to build up the best alignment by using

optimal alignments of smaller subsequences.

The Needleman-Wunsch algorithm is an example of

dynamic programming, a discipline invented by Richard
Bellman (an American mathematician) in 1953!

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How does dynamic programming work?

A divide-and-conquer strategy:
Break the problem into smaller subproblems.
Solve the smaller problems optimally.
Use the sub-problem solutions to construct an optimal
solution for the original problem.

Dynamic programming can be applied only to problems

exhibiting the properties of overlapping subproblems.
Examples include
Trevelling salesman problem
Finding the best chess move

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The mathematics

A matrix D(i, j) indexed by residues of each sequence is

built recursively, such that

 D(i − 1, j − 1) + s(xi , yj )

D(i, j) = max D(i − 1, j) + g

 D(i, j − 1) + g

subject to a boundary conditions. s(i, j) is the substitution

score for residues i and j, and g is the gap penalty.

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A walk-through: an overview

We consider all possible pairs of residue from two

sequences (this gives rise to a 2D matrix representation).

We will have two matrices: the score matrix and traceback

matrix.

The Needleman-Wunsch algorithm consists of three steps:

1. Initialisation of the score matrix
2. Calculation of scores and filling the traceback matrix
3. Deducing the alignment from the traceback matrix

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Consider the simple example

The alignment of two sequences SEND and AND with the

BLOSUM62 substitution matrix and gap opening penalty
of 10 (no gap extension):

SEND
-AND score: +1
A-ND score: +3 ← the best
AN-D score: -3
AND- score: -8

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 A

D
N
                              

                              

                              

                              

                              

                              

                              











                              

                              

                              

S

E

N

D

C(4,1) C(4,2) C(4,3) C(4,4) C(4,5)

C(3,1) C(3,2) C(3,3) C(3,4) C(3,5)
C(2,1) C(2,2) C(2,3) C(2,4) C(2,5)
C(1,1) C(1,2) C(1,3) C(1,4) C(1,5)

i = 1, 2, ..., N and j = 1, 2, ..., M
S
E
N
The score and traceback matrices

The cells of the score matrix are labelled C(i, j) where

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Initialization

The first row and the first column of the score and
traceback matrices are filled during the initialization.

S E N D S E N D

0 −10 −20 −30 −40 done left left left left

A −10 up

N −20 up

D −30 up

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Scoring

The score matrix cells are filled by row starting from the
cell C(2, 2)

The score of any cell C(i, j) is the maximum of:

qdiag = C(i − 1, j − 1) + S(i, j)

qup = C(i − 1, j) + g
qlef t = C(i, j − 1) + g

where S(i, j) is the substitution score for letters i and j,

and g is the gap penalty.

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Scoring– a pictorial representation

The value of the cell C(i, j) depends only on the values of

the immediately adjacent northwest diagonal, up, and left
cells:

C(i−1,j−1) C(i−1,j)

C(i,j−1) C(i,j)

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The Needleman-Wunsch progression

The first step is to calculate the value of C(2, 2):

S E N D S E N D

0 −10 −20 −30 −40 done left left left left

A −10 ? up ?

N −20 up

D −30 up

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The value of C(2, 2)

The calculation for the cell C(2, 2):

qdiag = C(1, 1) + S(S, A) = 0 + 1 = 1

qup = C(1, 2) + g = −10 + (−10) = −20
qlef t = C(2, 1) + g = −10 + (−10) = −20

Where C(1, 1), C(1, 2), and C(2, 1) are read from the
score matrix, and S(S, A) is the score for the S ↔ A
taken from the BLOSUM62 matrix.

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Filling the score and traceback matrices

For the score matrix C(2, 2) = qdiag which is 1. The

corresponding cell of the traceback matrix is ”diag”:

S E N D S E N D

0 −10 −20 −30 −40 done left left left left

A −10 1 up diag

N −20 up

D −30 up

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The progression is recursive

The next step is to calculate C(2, 3):

S E N D S E N D

0 −10 −20 −30 −40 done left left left left

A −10 1 ? up diag ?

N −20 up

D −30 up

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The value of C(2, 3)

The calculation for the cell C(2, 3)

qdiag = C(1, 2) + S(E, A) = −10 + −1 = −11

qup = C(1, 3) + g = −20 + (−10) = −30
qlef t = C(2, 2) + g = 1 + (−10) = −9

Thus C(2, 3) = −9 and the corresponding cell of the

traceback matrix is ”left”.

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The final score and traceback matrices

After all cells are filled, the score and traceback matrices
are:

S E N D S E N D

0 −10 −20 −30 −40 done left left left left

A −10 1 −9 −19 −29 up diag left left left

N −20 −9 −1 −3 −13 up diag diag diag left

D −30 −19 −11 2 3 up up diag diag diag

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The traceback

Traceback = the process of deduction of the best

alignment from the traceback matrix.

The traceback always begins with the last cell to be filled

with the score, i.e. the bottom right cell.

One moves according to the traceback value written in the

cell.

There are three possible moves: diagonally (toward the

top-left corner of the matrix), up, or left.

The traceback is completed when the first, top-left cell of

the matrix is reached (”done” cell).
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The traceback path
The traceback performed on the completed traceback
matrix:
S E N D
done left left left left

A up diag left left left

N up diag diag diag left

Traceback

D

up up diag diag diag

starts here

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The best alignment

The alignment is deduced from the values of cells along

the traceback path, by taking into account the values of
the cell in the traceback matrix:

diag – the letters from two sequences are aligned

left – a gap is introduced in the left sequence
up – a gap is introduced in the top sequence

Sequences are aligned backwards.

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The traceback step-by-step (1)

The first cell from the traceback path is ”diag” implying

that the corresponding letters are aligned:
D
D
S E N D
done left left left left

A up diag left left left

N up diag diag diag left

Traceback

D

up up diag diag diag

starts here

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The traceback step-by-step (2)

The second cell from the traceback path is also ”diag”

implying that the corresponding letters are aligned:
ND
ND
S E N D
done left left left left

A up diag left left left

N up diag diag diag left

Traceback

D

up up diag diag diag

starts here

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The traceback step-by-step (3)

The third cell from the traceback path is ”left” implying

the gap in the left sequence (i.e. we stay on the letter A
from the left sequence):
END
-ND
S E N D
done left left left left

A up diag left left left

N up diag diag diag left

Traceback

D

up up diag diag diag

starts here

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The traceback step-by-step (4)

The fourth cell from the traceback path is also ”diag”

implying that the corresponding letters are aligned. We
consider the letter A again, this time it is aligned with S:
SEND
A-ND
S E N D
done left left left left

A up diag left left left

N up diag diag diag left

Traceback

D

up up diag diag diag

starts here

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Compare with the exhaustive search

The best alignment via the Needleman-Wunsch algorithm:

SEND
A-ND

The exhaustive search:

SEND
-AND score: +1
A-ND score: +3 ← the best
AN-D score: -3
AND- score: -8

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A few observations

It was much easier to align SEND and AND by the

exhaustive search!

As we consider longer sequences the situation quickly

turns against the exhaustive search:
Two 12 residue sequences would require considering
∼ 1 million alignments.
Two 150 residue sequences would require considering
∼ 1088 alignments (∼ 1078 is the estimated number of
atoms in the Universe).

For two 150 residue sequences the Needleman-Wunsch

algorithm requires filling a 150 × 150 matrix.
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The summary

The alignment is over the entire length of two sequences:

the traceback starts from the lower right corner of the
traceback matrix, and completes in the upper left cell of
the matrix.

The Needleman-Wunsch algorithm works in the same way

regardless of the length or complexity of sequences, and
guarantees to find the best alignment.

The Needleman-Wunsch algorithm is appropriate for

finding the best alignment of two sequences which are (i)
of the similar length; (ii) similar across their entire lengths.

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