CAP5510 – Bioinformatics

Substitution Patterns
Tamer Kahveci
CISE Department
University of Florida

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 Goals
• Understand how mutations occur
• Learn models for predicting the number of
mutations
• Understand why scoring matrices are used
and how they are derived
• Learn major scoring matrices

2
 Why Substitute Patterns ?
• Mutations happen because of mistakes in DNA
replication and repair.
• Our genetic code changes due to mutations
– Insert, delete, replace
• Three types of mutations
– Advantageous
– Disadvantageous
– Neutral
• We only observe substitutions that passed
selection process

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 Mutation Rates

Parent Organism

T time R = K/(2T)

Organism A Organism B

K: number of substitutions

4
 Functional Constraints
• Functional sites are less likely to mutate
– Noncoding = 3.33 (subs/109 yr)
– Coding = 1.58 (subs/109 yr)
• Indels about 10 times less likely than
substitutions

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Nucleotide Substitutions and Amino
Acids
• Synonymous substitutions do not change amino acids
• Nonsynonymous do change
• Degeneracy
– Fourfold degenerate: gly = {GGG, GGA, GGU, GGC}
– Twofold degenerate: asp = {GAU, GAC}, glu = {GAA, GAG}
– Non-degenerate: phe = UUU, leu = CUU, ile = AUU, val = GUU
• Example substitution rates in human and mouse
– Fourfold degenerate: 2.35
– Twofold degenerate: 1.67
– Non-degenerate: 0.56

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Predicting Substitutions

How can we count the true

number of substitutions ?

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 Jukes-Cantor Model
• Each nucleotide can change into another
one with the same probability
P(A->A’, 1) = x, for each A’
P(A->A, 1) = 1 – 3x
Compute P(A->A’, 2) & P(A->A, 2)
x
A C P(A->A, t+1) = 3 P(A->A’, t) P(A’->A, 1) +
x P(A->A, t) P(A->A, 1)
x
P(A->A, t) ~ ¼ + (3/4)e-4ft
G T
K = num. subst. = -¾ ln(1 – f4/3), f =
fraction of observed substitutions

Oversimplification 8
 Two Parameter Model
• Transition:
– purine->purine (A, G), Purine
pyrimidine->pyrimidine (C,
T)
• Transversion:
– purine <-> pyrimidine
• Transitions are more
likely than transversions.
• Use different probabilities
Pyrimidine
for transitions and
transversions.

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 Two Parameter Model
•P(AA,1) = 1-x-2y P(AA,2) = (1-x-2y) P(AA,1) + x P(AG,1) + y
•Compute P(AA,2) P(AC,1) + y P(AT,1)

y P(AA,t) = ¼ + ¼ e-4yt + ½ e-2(x+y)t

A C
y K = ½ ln(1/(1-2P-Q)) + ¼ ln(1/(1-2Q))
x
P,Q: fraction of transitions and transversions
G T observed.

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 More Parameters ?
• Assign a different probability for each pair
of nucleotides
• Not harder to compute than simpler
models
• Not necessarily better than simpler models

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 Amino Acid substitutions (1)
• Harder to model than nucleotides
– An amino acid can be substituted for another in more
than one ways
– The number of nucleotide substitutions needed to
transform one amino acid to another may differ
• Pro = CCC, leu = CUC, ile = AUC
– The likelihood of nucleotide substitutions may differ
• Asp = GAU, asn = AAU, his = CAU
– Amino acid substitutions may have different effects on
the protein function

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 Amino Acid substitutions (2)
• Mutation rates may vary greatly among
genes
– Nonsynonymous substitution may affect
functionality with smaller probability in some
genes
• Molecular clock (Zuckerlandl, Paulding)
– Mutation rates may be different for different
organisms, but it remains almost constant
over the time.

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Scoring Matrices

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 What is it & why ?
• Let alphabet contain N letters
– N = 4 and 20 for nucleotides and amino acids
• N x N matrix
• (i,j) shows the relationship between ith and jth
letters.
– Positive number if letter i is likely to mutate into letter j
– Negative otherwise
– Magnitude shows the degree of proximity
• Symmetric

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 The BLOSUM45 Matrix
A R N D C Q E G H I L K M F P S T W Y V
A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0
R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2
N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3
D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3
C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1
Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3
E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3
G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3
H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3
I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3
L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1
K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2
M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1
F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0
P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3
S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1
T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0
W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3
Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 16
V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5
 Scoring Matrices for DNA
A C G T
A C G T A C G T
A 1 -3 -3 -3
A 1 0 0 0 A 1 -5 -1 -5
C -3 1 -3 -3
C 0 1 0 0 C -5 1 -5 -1
G -3 -3 1 -3
G 0 0 1 0 G -1 -5 1 -5
T -3 -3 -3 1
T 0 0 0 1 T -5 -1 -5 1

identity BLAST Transitions &

transversions

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 Scoring Matrices for Amino Acids
• Chemical similarities
– Non-polar, Hydrophobic (G, A, V, L, I, M, F, W, P)
– Polar, Hydrophilic (S, T, C, Y, N, Q)
– Electrically charged (D, E, K, R, H)
– Requires expert knowledge
• Genetic code: Nucleotide substitutions
– E: GAA, GAG
– D: GAU, GAC
– F: UUU, UUC
• Actual substitutions
– PAM
– BLOSUM

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 Scoring Matrices: Actual
Substitutions
• Manually align proteins
• Look for amino acid substitutions
• Entry ~ log(freq(observed)/freq(expected))
• Log-odds matrices

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PAM Matrices

(Dayhoff 1972)

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 PAM
• PAM = “Point Accepted Mutation”
interested only in mutations that have
been “accepted” by natural selection
• An accepted mutation is a mutation that
occurred and was positively selected by
the environment; that is, it did not cause
the demise of the particular organism
where it occurred.

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 Interpretation of PAM matrices
• PAM-1 : one substitution per 100 residues (a
PAM unit of time)
• “Suppose I start with a given polypeptide sequence M at
time t, and observe the evolutionary changes in the
sequence until 1% of all amino acid residues have
undergone substitutions at time t+n. Let the new
sequence at time t+n be called M’. What is the probability
that a residue of type j in M will be replaced by i in M’?”
• PAM-K : K PAM time units

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 PAM Matrices (1)
• Starts with a multiple sequence alignment
of very similar (>85% identity) proteins.
Assumed to be homologous
• Compute the relative mutability, mi, of
each amino acid
– e.g. mA = how many times was alanine
substituted with anything else on the
average?

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 Relative Mutability
• ACGCTAFKI
GCGCTAFKI
ACGCTAFKL
GCGCTGFKI
GCGCTLFKI
ASGCTAFKL
ACACTAFKL
• Across all pairs of sequences, there are 28
A  X substitutions
• There are 10 ALA residues, so mA = 2.8

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 Pam Matrices (2)
• Construct a phylogenetic tree for the sequences in the
alignment

AG
ACGCTAFKI
IL
FG,A = 3
GCGCTAFKI ACGCTAFKL

AG AL CS GA

GCGCTGFKI GCGCTLFKI ASGCTAFKL ACACTAFKL

• Calculate substitution frequencies FX,X

• Substitutions may have occurred either way, so A  G
also counts as G  A. 25
 Mutation Probabilities
• Mi,j represents the probability of J  I
substitution.

ACGCTAFKI
AG IL

GCGCTAFKI ACGCTAFKL

AG AL CS GA

GCGCTGFKI GCGCTLFKI ASGCTAFKL ACACTAFKL

m j Fij 2.8  3 = 2.1

M ij  M G, A 
 Fij
i
4
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 The PAM Matrix
• The entries of the scoring matrix are the
Mi,j values divided by the frequency of
occurrence, fi, of residue i.
• fG = 10 GLY / 63 residues = 0.1587
• RG,A = log(2.1/0.1587) = log(12.760) = 1.106
• Log-odds matrix
• Diagonal entries are Mjj = 1– mj
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 Computation of PAM-K
• Assume that changes at time T+1 are
independent of the changes at time T.
• Markov chain
• P(A-->B) = X P(A->X) P(X->B)
• PAM-K = (PAM-1)K
• PAM-250 is most commonly used

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 PAM - Discussion
• Smaller K, PAM-K is better for closely related
sequences, large K is better for distantly related
sequences
• Biased towards closely related sequences since it starts
from highly similar sequences (BLOSUM solves this)
• If Mi,j is very small, we may not have a large enough
sample to estimate the real probability. When we
multiply the PAM matrices many times, the error is
magnified.
• Mutation rate may change from one gene to another

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BLOSUM Matrices

Henikoff & Henikoff 1992

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 BLOSUM Matrix
• Begin with a set of protein sequences and obtain blocks.
– ~2000 blocks from 500 families of related proteins
– More data than PAM
• A block is the ungapped alignment of a highly conserved region of a
family of proteins.
• MOTIF program is used to find blocks
• Substitutions in these blocks are used to compute BLOSUM matrix

block 1 block 2 block 3

WWYIR CASILRKIYIYGPV GVSRLRTAYGGRKNRG

WFYVR … CASILRHLYHRSPA … GVGSITKIYGGRKRNG
WYYVR AAAVARHIYLRKTV GVGRLRKVHGSTKNRG
WYFIR AASICRHLYIRSPA GIGSFEKIYGGRRRRG
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 Constructing the Matrix
• Count the frequency of occurrence of each amino acid. This gives
the background distribution pa
• Count the number of times amino acid a is aligned with amino acid
b: fab
– A block of width w and depth s contributes ws(s-1)/2 = np pairs
• Compute the occurrence probability of each pair
– qab = fab/ np
• Compute the
i
probability of occurrence of amino acid a
– pa = qaa + Σ
a≠b qab /2

• Compute the expected probability of occurrence of each pair

– eab = 2papb, if a ≠ b
papb otherwise
• Compute the log likelihood ratios, normalize, and round.
– 2* log2 qab / eab

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 Constructing the Matrix: Example
• fAA = 36, fAS = 9
• Observed frequencies of pairs
– qAA = fAA/(fAA+fAS) = 36/45 = 0.8
– qAS = 9/45 = 0.2
A
A • Expected frequencies of letters
– pA = qAA + qAS/2 = 0.9
A
– pS = qAS/2 = 0.1
A • Expected frequencies of pairs
S – eAA = pA x pA = 0.81
… A … – eAS = 2 x pA x pS = 0.18
A • Matrix entries
A – MAA = 2x log2(qAA/eAA) = -0.04 ~ 0
A – MAS = 2 x log2(qAS/eAS) = 0.3 ~ 0
A

9A, 1S
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 Computation of BLOSUM-K
• Different levels of the BLOSUM matrix can be created by
differentially weighting the degree of similarity between
sequences. For example, a BLOSUM62 matrix is
calculated from protein blocks such that if two
sequences are more than 62% identical, then the
contribution of these sequences is weighted to sum to
one. In this
a b
way the contributions of multiple entries of
closely related sequences is reduced.
• Larger numbers used to measure recent divergence,
default is BLOSUM62

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BLOSUM 62 Matrix
Check scores for

MILV
-small hydrophobic

NDEQ
-acid, hydrophilic

HRK
-basic

FYW
-aromatic

STPAG
-small hydrophilic

C
-sulphydryl
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 PAM vs. BLOSUM

Equivalent PAM and BLOSSUM matrices:

PAM100 = Blosum90
PAM120 = Blosum80
PAM160 = Blosum60
PAM200 = Blosum52
PAM250 = Blosum45

BLOSUM62 is the default matrix to use.

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 PAM vs. BLOSUM

PAM BLOSUM

Built from global alignments Built from local alignments

Built from small amout of Data Built from vast amout of Data
Counting is based on minimum Counting based on groups of
replacement or maximum parsimony related sequences counted as one
Perform better for finding global Better for finding local
alignments and remote homologs alignments
Higher PAM series means more Lower BLOSUM series means
divergence more divergence

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