OCCBIO 2006 Tutorial
Fundamental Concepts of
Bioinformatics
Michael L. Raymer
Computer Science, Biomedical Sciences
Wright State University
Bioinformatics Research Group
Part I – Background
Some basics of molecular biology,
and some of the fundamental
problems facing bioinformaticians
The Central Dogma of molecular biology
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DNA structure and base pairing
 Polymer of:
• Ribose sugar
• Phosphate
• Nitrogenous base
 Four bases
• A, C, G, T
 Base pairing
• A—T
• G—C
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DNA is an information carrying molecule
 Arranged into 23
chromosome pairs in the
nucleus of each cell
 Genes: coding
information
• < 5% of all DNA
• Instructions for protein
synthesis
• Directions on when and
where to synthesize
proteins (regulatory
regions)
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The Genetic Code
 Redundancy/robustness
•
•
•
•
Synonymous codons
Dual strands
Diploidy
Amino acid structure (?)
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Transcription
DNA
transcription

RNA
translation

Protein
Messenger RNA
 Carries
instructions
for a protein
outside of the
nucleus to the
ribosome
 The ribosome
is a protein
complex that
synthesizes
new proteins
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Prokaryotic gene structure
Yeast RNA Polymerase II
Darst et al. in 1991 (Cell 66, pp 121-128)
5' UTR
3' UTR
5'
3'
Coding
Operator: regulation
Stop Codon
Promoter: RNA polymerase binding
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Regulation of transcription
 Energy budget
 Cellular differentiation & tissue function
From W. Becker, L. Kleinsmith, and J. Hardin, The World of the Cell, Fourth Edition. Copyright © Addison Wesley Longman, Inc.
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Bioinformatics problems
 Shotgun sequencing
 Sequence alignment & multiple alignment
• Database searches
 Phylogenetic tree induction
 Protein structure determination, modeling, and
prediction
 Ligand screening and docking
 Many, many more
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Bioinformatics data
 DNA sequence information
• Genome projects, etc.
 mRNA expression information
• Microarrays, SAGE
 Metabolite concentrations
• Mass Spec., NMR Spec., etc.
 Protein sequence information
 Protein structure information
• X-Ray Crystallography
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Part II – Obtaining Sequences
Sanger Sequencing
Primer Walking
Shotgun Approaches
Fragment Assembly Algorithms
Outline




PCR
Sanger Sequencing
Primer Walking
Shotgun Sequencing
• Models
• Algorithms
• Analysis
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Polymerase chain reaction (PCR)
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Gel electrophoresis
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Sanger sequencing
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Limitations to sequencing
 You must have a primer of known sequence to
initiate PCR
 Only about 1000nts can be sequenced in a
single reaction
 The sequencing process is slow, so it is
beneficial to do as much in parallel as possible
• Primer hopping
• Shotgun approach
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Shotgun Sequencing
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The Ideal Case
 Find maximal overlaps between fragments:
ACCGT
CGTGC
TTAC
TACCGT
--ACCGT-----CGTGC
TTAC-----TACCGT—
TTACCGTGC
Consensus
sequence
determined by vote
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Quality Metrics
 The coverage at position i of the target or
consensus sequence is the number of fragments
that overlap that position
Target:
No coverage
 Two contigs
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Quality Metrics
 Linkage – the degree of overlap between
fragments
Target:
Perfect coverage, poor average linkage
poor minimum linkage
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Real World Complications
 Base call errors
 Chimeric fragments, contamination (e.g. from
the vector)
--ACCGT-----CGTGC
TTAC-----TGCCGT—
TTACCGTGC
Base Call Error
--ACC-GT-----CAGTGC
TTAC------TACC-GT—
TTACC-GTGC
Insertion Error
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--ACCGT-----CGTGC
TTAC-----TAC-GT—
TTACCGTGC
Deletion Error
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Unknown Orientation
A fragment can come
from either strand
CACGT
ACGT
ACTACG
GTACT
ACTGA
CTGA
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





CACGT
-ACGT
--CGTAGT
-----AGTAC
--------ACTGA
---------CTGA
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Repeats
 Direct repeats
A
X
A
X
B
C
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X
X
C
B
X
D
X
D
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Repeats
 Direct repeats
A
X
A
X
B
D
Y
Y
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C
C
X
X
D
B
Y
E
Y
E
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Repeats
 Inverted repeats
X
X
X
X
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Sequence Alignment Models
 Shortest common superstring
• Input: A collection, F, of strings (fragments)
• Output: A shortest possible string S such that for
every f  F, S is a superstring of f.
 Example:
• F = {ACT, CTA, AGT}
• S = ACTAGT
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Problems with the SCS model
x
x
x




x´
Directionality of fragments must be known
No consideration of coverage
Some simple consideration of linkage
No consideration of base call errors
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Reconstruction
 Deals with errors and unknown orientation
 Definitions
• f is an approximate substring of S at error level 
when ds(f, S)    | f |
Match = 0
• ds = substring edit distance:
 Reconstruction
Mismatch = 1
Gap = 1
• Input: A collection, F, of strings, and a tolerance
level, 
• Output: Shortest possible string, S, such that for
every f  F : minds  f , S , ds  f , S    f
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Reconstruction Example
 Input:
 Output:
F = {ATCAT, GTCG, CGAG, TACCA}
 = 0.25
ATGAT
------CGAC
-CGAG
----TACCA
ACGATACGAC
ATCAT
GTCG
ds(CGAG, ACGATACGAC) = 1
= 0.25  4
So this output is OK for  = 0.25
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Gaps in Reconstruction
 Reconstruction allows gaps in fragments:
AT-GA----ATCGATAGAC
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ds = 1
32
Limitations of Reconstruction





Models errors and unknown orientation
Doesn’t handle repeats
Doesn’t model coverage
Only handles linkage in a very simple way
Always produces a single contig
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Contigs
 Sometimes you just can’t put all of the
fragments together into one contiguous
sequence:
No way to tell how
much sequence is
missing between
them.
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?
No way to tell the
order of these two
contigs.
34
Multicontig
 Definitions
• A layout, L, is a multiple alignment of the fragments

Columns numbered from 1 to |L |
• Endpoints of a fragment: l(f) and r(f)
• An overlap is a link is no other fragment completely
covers the overlap
Link
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Not a link
35
Multicontig
 More definitions
• The size of a link is the number of overlapping
positions
ACGTATAGCATGA
GTA
CATGATCA
ACGTATAG
GATCA
A link of size 5
• The weakest link is the smallest link in the layout
• A t-contig has a weakest link of size t
• A collection, F, admits a t-contig if a t-contig can be
constructed from the fragments in F
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Perfect Multicontig
 Input: F, and t
 Output: a minimum number of collections, Ci,
such that every Ci admits a t-contig
Let F = {GTAC, TAATG, TGTAA}
t=3
t=1
--TAATG
TGTAA--
TGTAA------TAATG--------GTAC
GTAC
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Handling errors in Multicontig
 The image of a fragment is the portion of the
consensus sequence, S, corresponding to the
fragment in the layout
 S is an -consensus for a collection of
fragments when the edit distance from each
fragment, f, and its image is at most   | f |
TATAGCATCAT
CGTC
CATGATCA
ACGGATAG
GTCCA
ACGTATAGCATGATCA
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An -consensus
for  = 0.4
38
Definition of Multicontig
 Input: A collection, F , of strings, an integer t 
0, and an error tolerance  between 0 and 1
 Output: A partition of F into the minimum
number of collections Ci such that every Ci
admits a t-contig with an -consensus
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Example of Multicontig
 Let  = 0.4, t = 3
TATAGCATCAT
ACGTC
CATGATCAG
ACGGATAG
GTCCAG
ACGTATAGCATGATCAG
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Algorithms
 Most of the algorithms to solve the fragment
assembly problem are based on a graph model
 A graph, G, is a collection of edges, e, and
vertices, v.
• Directed or undirected
• Weighted or unweighted
 We will discuss
representations and
other issues shortly…
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A directed,
unweighted
graph
41
The Maximum Overlap Graph
 The text calls it an overlap multigraph
 Each directed edge, (u,v) is weighted with the
length of the maximal overlap between a suffix
of u and a prefix of v
TACGA
a
1
2
ACCC
CTAAAG
b
1
c
1
1
d
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GACA
0-weight
edges
omitted!
42
Paths and Layouts
 The path dbc leads to the alignment:
GACA----------ACCC----------CTAAAG
TACGA
a
1
2
ACCC
CTAAAG
c
1
1
d
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b
1
GACA
43
Superstrings
 Every path that covers every node is a
superstring
 Zero weight edges result in alignments like:
GACA-----------GCCC------------TTAAAG
 Higher weights produce more overlap, and thus
shorter strings
 The shortest common superstring is the highest
weight path that covers every node
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Graph formulation of SCS
 Input: A weighted, directed graph
 Output: The highest-weight path that touches
every node of the graph
Does this problem sound familiar?
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The Greedy Algorithm
Algorithm greedy
Sort edges in decreasing weight order
For each edge in this order
If the edge does not form a cycle
and the edge does not start or end at
the same node as another edge in the set
then
add the edge to the current set
End for
End Algorithm
Figure 4.16, page 125
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Greedy Example
7
4
5
2
2
2
6
3
1
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Greedy does not always find the best path
GCC
2
ATGC
0
2
TGCAT
3
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Tools for Shotgun Sequencing
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Common Difficulty
 Each of these problems is a method for
modeling fragment assembly
 Each of these problems is provably intractable
 How?
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Embedding problems

Suppose I told you that I had found a clever
way to model the TSP as a shortest common
superstring problem
•
•

Paths between cities are represented as fragments
The shortest path is the shortest common
superstring of the fragments
If this is true, then there are only two
possibilities:
1. This problem is just as intractable as TSP
2. TSP is actually a tractable problem!
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NP-Complete Problems
 There is a collection of problems that computer
scientists believe to be intractable
• TSP is one of them
 Each of them has been modeled as one or more
of the other NP-complete problems
 If you solve one, you solve them all
 A problem, p, is NP-hard if you can model one
of these NP-complete problems as an instance
of p
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NP-Completeness
NP
Subset sum
3-SAT
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TSP
P
53
P = NP?
NP
Subset sum
3-SAT
NP
P
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Part III – Sequence Alignments
Needleman-Wunsch
Smith-Waterman
Dynamic Programming
Why align sequences?
 The draft human genome is available
 Automated gene finding is possible
 Gene: AGTACGTATCGTATAGCGTAA
• What does it do?
 One approach: Is there a similar gene in
another species?
• Align sequences with known genes
• Find the gene with the “best” match
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Comparing two sequences
 Point mutations, easy:
ACGTCTGATACGCCGTATAGTCTATCT
ACGTCTGATTCGCCCTATCGTCTATCT
 Indels are difficult, must align sequences:
ACGTCTGATACGCCGTATAGTCTATCT
CTGATTCGCATCGTCTATCT
ACGTCTGATACGCCGTATAGTCTATCT
----CTGATTCGC---ATCGTCTATCT
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Scoring a sequence alignment
 Match score:
+1
 Mismatch score:
+0
 Gap penalty:
–1
ACGTCTGATACGCCGTATAGTCTATCT
||||| |||
|| ||||||||
----CTGATTCGC---ATCGTCTATCT
 Matches: 18 × (+1)
 Mismatches: 2 × 0
 Gaps: 7 × (– 1)
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Score = +11
58
DNA Replication
 Prior to cell division, all the
genetic instructions must be
“copied” so that each new cell
will have a complete set
 DNA polymerase is the enzyme
that copies DNA
• Synthesizes in the 5' to 3' direction
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Over time, genes accumulate mutations
 Environmental factors
• Radiation
• Oxidation
 Mistakes in replication or
repair
 Deletions, Duplications
 Insertions
 Inversions
 Point mutations
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Deletions
 Codon deletion:
ACG ATA GCG TAT GTA TAG CCG…
• Effect depends on the protein, position, etc.
• Almost always deleterious
• Sometimes lethal
 Frame shift mutation:
ACG ATA GCG TAT GTA TAG CCG…
ACG ATA GCG ATG TAT AGC CG?…
• Almost always lethal
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Indels
 Comparing two genes it is generally impossible
to tell if an indel is an insertion in one gene, or
a deletion in another, unless ancestry is known:
ACGTCTGATACGCCGTATCGTCTATCT
ACGTCTGAT---CCGTATCGTCTATCT
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Origination and length penalties
 We want to find alignments that are
evolutionarily likely.
 Which of the following alignments seems more
likely to you?
ACGTCTGATACGCCGTATAGTCTATCT
ACGTCTGAT-------ATAGTCTATCT

ACGTCTGATACGCCGTATAGTCTATCT
AC-T-TGA--CG-CGT-TA-TCTATCT

 We can achieve this by penalizing more for a
new gap, than for extending an existing gap
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Scoring a sequence alignment (2)
 Match/mismatch score:
+1/+0
 Origination/length penalty:
–2/–1
ACGTCTGATACGCCGTATAGTCTATCT
||||| |||
|| ||||||||
----CTGATTCGC---ATCGTCTATCT




Matches: 18 × (+1)
Mismatches: 2 × 0
Origination: 2 × (–2)
Length: 7 × (–1)
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Score = +7
64
How can we find an optimal alignment?
 Finding the alignment is computationally hard:
ACGTCTGATACGCCGTATAGTCTATCT
CTGAT---TCG—CATCGTC--T-ATCT
 C(27,7) gap positions = ~888,000 possibilities
 It’s possible, as long as we don’t repeat our
work!
 Dynamic programming: The Needleman &
Wunsch algorithm
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What is the optimal alignment?
 ACTCG
ACAGTAG
 Match: +1
 Mismatch: 0
 Gap: –1
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Needleman-Wunsch: Step 1
 Each sequence along one axis
 Mismatch penalty multiples in first row/column
 0 in [1,1] (or [0,0] for the CS-minded)
A
C
A
G
T
A
G
0
-1
-2
-3
-4
-5
-6
-7
A
-1
1
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C
-2
T
-3
C
-4
G
-5
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Needleman-Wunsch: Step 2
 Vertical/Horiz. move: Score + (simple) gap penalty
 Diagonal move: Score + match/mismatch score
 Take the MAX of the three possibilities
A
C
A
G
T
A
G
0
-1
-2
-3
-4
-5
-6
-7
A
-1
1
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C
-2
T
-3
C
-4
G
-5
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Needleman-Wunsch: Step 2 (cont’d)
 Fill out the rest of the table likewise…
a
a
c
a
g
t
a
g
0
-1
-2
-3
-4
-5
-6
-7
c
-1
1
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t
-2
0
c
-3
-1
g
-4
-2
-5
-3
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Needleman-Wunsch: Step 2 (cont’d)
 Fill out the rest of the table likewise…
a
a
c
a
g
t
a
g
0
-1
-2
-3
-4
-5
-6
-7
c
-1
1
0
-1
-2
-3
-4
-5
t
-2
0
2
1
0
-1
-2
-3
c
-3
-1
1
2
1
1
0
-1
g
-4
-2
0
1
2
1
1
0
-5
-3
-1
0
2
2
1
2
 The optimal alignment score is calculated in the
lower-right corner
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But what is the optimal alignment
 To reconstruct the optimal alignment, we must
determine of where the MAX at each step came
from…
a
a
c
a
g
t
a
g
0
-1
-2
-3
-4
-5
-6
-7
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c
-1
1
0
-1
-2
-3
-4
-5
t
-2
0
2
1
0
-1
-2
-3
c
-3
-1
1
2
1
1
0
-1
g
-4
-2
0
1
2
1
1
0
-5
-3
-1
0
2
2
1
2
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A path corresponds to an alignment

= GAP in top sequence

= GAP in left sequence

= ALIGN both positions
 One path from the previous table:
 Corresponding alignment (start at the end):
AC--TCG
ACAGTAG
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Score = +2
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Practice Problem
 Find an optimal alignment for these two
sequences:
GCGGTT
GCGT
 Match: +1
 Mismatch: 0
 Gap: –1 g
c
g
t
g
0
-1
-2
-3
-4
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c
-1
g
-2
g
-3
t
-4
t
-5
-6
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Practice Problem
 Find an optimal alignment for these two
sequences:
GCGGTT
GCGT
g
c
g
g
t
t
g
c
g
t
0
-1
-2
-3
-4
-1
1
0
-1
-2
-2
0
2
1
0
-3
-1
1
3
2
GCGGTT
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-4
-2
0
2
3
-5
-3
-1
1
3
-6
-4
-2
0
2
Score = +2
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Semi-global alignment
 Suppose we are aligning:
GCG
GGCG
 Which do you prefer?
G-CG
-GCG
GGCG
GGCG
g
g
g
c
g
0
-1
-2
-3
-4
c
-1
1
0
-1
-2
g
-2
0
1
1
0
-3
-1
1
1
2
 Semi-global alignment allows gaps at the ends
for free.
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Semi-global alignment
 Semi-global alignment allows gaps at the ends
for free.
g
g
g
c
g
0
0
0
0
0
c
0
1
1
0
1
g
0
0
1
2
1
0
1
1
1
3
 Initialize first row and column to all 0’s
 Allow free horizontal/vertical moves in last
row and column
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Local alignment
 Global alignments – score the entire alignment
 Semi-global alignments – allow unscored gaps
at the beginning or end of either sequence
 Local alignment – find the best matching
subsequence
 CGATG
AAATGGA
 This is achieved by allowing a 4th alternative at
each position in the table: zero.
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Local alignment
 Mismatch = –1 this time
c
a
a
a
t
g
g
a
0
-1
-2
-3
-4
-5
-6
-7
g
-1
0
0
0
0
0
0
0
a
-2
0
0
0
0
1
1
0
t
-3
0
1
1
0
0
0
2
g
-4
0
0
0
2
1
0
1
-5
0
0
0
1
3
2
1
CGATG
AAATGGA
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Optimal Substructure in Alignments
 Consider the alignment:
ACGTCTGATACGCCGTATAGTCTATCT
||||| |||
|| ||||||||
----CTGATTCGC---ATCGTCTATCT
 Is it true that the alignment in the boxed region
must be optimal?
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A Greedy Strategy
 Consider this pair of sequences
GAGC
GAP = 1
CAGC
 Greedy Approach:
G or G or
C
 Leads to
GAGC-----CAGC
Match = +1
G
Better:
OCCBIO 2006 – Fundamental Bioinformatics
Mismatch = 2
GACG
CACG
80
Breaking apart the problem
 Suppose we are aligning:
ACTCG
ACAGTAG
 First position choices:
A
A
+1
CTCG
CAGTAG
A
-
-1
CTCG
ACAGTAG
A
-1
ACTCG
CAGTAG
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A Recursive Approach to Alignment
 Choose the best alignment based on these three
possibilities:
align(seq1, seq2) {
if (both sequences empty) {return 0;}
if (one string empty) {
return(gapscore * num chars in nonempty seq);
else {
score1 = score(firstchar(seq1),firstchar(seq2))
+ align(tail(seq1), tail(seq2));
score2 = align(tail(seq1), seq2) + gapscore;
score3 = align(seq1, tail(seq2) + gapscore;
return(min(score1, score2, score3));
}
}
}
OCCBIO 2006 – Fundamental Bioinformatics
82
Time Complexity of RecurseAlign
 What is the recurrence equation for the time
needed by RecurseAlign?
T (n)  3T (n  1)  3
3
n
3
3
3
…
3
3
9
3
27
n
3
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83
RecurseAlign repeats its work
A
C
G
T
A
T
C
G
C
G
T
A
T
A
G
A
T
G
C
T
C
T
C
G
OCCBIO 2006 – Fundamental Bioinformatics
84
Dynamic Programming
 Remember all the subproblem answers along the way:
a
a
c
a
g
t
a
g
0
-1
-2
-3
-4
-5
-6
-7
c
-1
1
0
-1
-2
-3
-4
-5
t
-2
0
2
1
0
-1
-2
-3
c
-3
-1
1
2
1
1
0
-1
g
-4
-2
0
1
2
1
1
0
-5
-3
-1
0
2
2
1
2
 This is possible for any problem that exhibits
optimal substructure
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85
Saving Space
 Note that we can throw away the previous rows
of the table as we fill it in:
a
This row
is based
only on
this one
a
c
a
g
t
a
g
OCCBIO 2006 – Fundamental Bioinformatics
0
-1
-2
-3
-4
-5
-6
-7
c
-1
1
0
-1
-2
-3
-4
-5
t
-2
0
2
1
0
-1
-2
-3
c
-3
-1
1
2
1
1
0
-1
g
-4
-2
0
1
2
1
1
0
-5
-3
-1
0
2
2
1
2
86
Saving Space (2)
 Each row of the table contains the scores for
aligning a prefix of the left-hand sequence with
all prefixes of the top sequence:
a
Scores for
aligning
aca with
all
prefixes of
actcg
a
c
a
g
t
a
g
OCCBIO 2006 – Fundamental Bioinformatics
0
-1
-2
-3
-4
-5
-6
-7
c
-1
1
0
-1
-2
-3
-4
-5
t
-2
0
2
1
0
-1
-2
-3
c
-3
-1
1
2
1
1
0
-1
g
-4
-2
0
1
2
1
1
0
-5
-3
-1
0
2
2
1
2
87
Divide and Conquer
 By using a recursive approach, we can use only
two rows of the matrix at a time:
• Choose the middle character of the top sequence, i
• Find out where i aligns to the bottom sequence

Needs two vectors of scores
• Recursively align the sequences before and after the
fixed positions
i
ACGCTATGCTCATAG
CGACGCTCATCG
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Finding where i lines up
 Find out where i aligns to the bottom sequence

Needs two vectors of scores
i
s: ACGCTATGCTCATAG
t: CGACGCTCATCG
 Assuming i lines up with a character:
alignscore = align(ACGCTAT, prefix(t)) + score(G, char from t)
+ align(CTCATAG, suffix(t))
 Which character is best?
• Can quickly find out the score for aligning ACGCTAT with
every prefix of t.
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89
Finding where i lines up
 But, i may also line up with a gap
i
s: ACGCTATGCTCATAG
t: CGACGCTCATCG
 Assuming i lines up with a gap:
alignscore = align(ACGCTAT, prefix(t)) + gapscore
+ align(CTCATAG, suffix(t))
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Recursive Call
 Fix the best position for I
 Call align recursively for the prefixes and
suffixes:
i
s: ACGCTATGCTCATAG
t:
CGACGCTCATCG
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91
Complexity
 Let len(s) = m and len(t) = n
i
 Space: 2m
s: ACGCTATGCTCATAG
 Time:
t:
CGACGCTCATCG
• Each call to build
similarity vector = m´n´
• First call + recursive call:
mn mn
m
T m, n  

T ,
2
2
2
j

m
j T ,n 

2

j

 m n  m j  m( n  j )
 2m n
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General Gap Penalties
 Suppose we are no longer using simple gap
penalties:
• Origination = −2
• Length = −1
 Consider the last position of the alignment for
ACGTA with ACG
 We can’t determine the score for
G
or
G
unless we know the previous positions!
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Scoring Blocks
 Now we must score a block at a time
A A C --- A TATCCG A C T AC
A C T ACC T ------ C G C --
 A block is a pair of characters, or a maximal
group of gaps paired with characters
 To score a position, we need to either start a
new block or add it to a previous block
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The Algorithm
 Three tables
• a – scores for alignments ending in char-char blocks
• b – scores for alignments ending in gaps in the top
sequence (s)
• c – scores for alignments ending in gaps in the left
sequence (t)
 Scores no longer depend on only three
positions, because we can put any number of
gaps into the last block
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The Recurrences
ai  1, j  1

ai, j   p i, j   maxbi  1, j  1
ci  1, j  1

ai, j  k   wk , for1  k  j
bi, j   max
ci, j  k   wk , for1  k  j
ai  k , j   wk , for1  k  i
ci, j   max
bi  k , j   wk , for1  k  i
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The Optimal Alignment
 The optimal alignment is found by looking at
the maximal value in the lower right of all three
arrays
 The algorithm runs in O(n3) time
• Uses O(n2) space
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Part IV – Database Searches
BLAST
Search statistics
Database Searching
 How can we find a particular short sequence in
a database of sequences (or one HUGE
sequence)?
 Problem is identical to local sequence
alignment, but on a much larger scale.
 We must also have some idea of the
significance of a database hit.
• Databases always return some kind of hit, how
much attention should be paid to the result?
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BLAST
 BLAST – Basic Local Alignment Search Tool
 An approximation of the Needleman & Wunsch
algorithm
 Sacrifices some search sensitivity for speed
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100
Scoring Matrices
 DNA
 Proteins
• Identity
• Transition/Transversion
A
R
N
D
C
Q
E
G
H
I
L
K
M
F
P
S
T
W
Y
V
A
2
-2
0
0
-2
0
0
1
-1
-1
-2
-1
-1
-4
1
1
1
-6
-3
0
• PAM
• BLOSUM
R
N
D
C
Q
E
G
H
I
L
K
M
F
P
S
T
W
Y
V
6
0
-1
-4
1
-1
-3
2
-2
-3
3
0
-4
0
0
-1
2
-4
-2
2
2
-4
1
1
0
2
-2
-3
1
-2
-4
-1
1
0
-4
-2
-2
4
-5
2
3
1
1
-2
-4
0
-3
-6
-1
0
0
-7
-4
-2
4
-5
-5
-3
-3
-2
-6
-5
-5
-4
-3
0
-2
-8
0
-2
4
2
-1
3
-2
-2
1
-1
-5
0
-1
-1
-5
-4
-2
4
0
1
-2
-3
0
-2
-5
-1
0
0
-7
-4
-2
5
-2
-3
-4
-2
-3
-5
-1
1
0
-7
-5
-1
6
-2
-2
0
-2
-2
0
-1
-1
-3
0
-2
5
2
-2
2
1
-2
-1
0
-5
-1
4
6
-3
4
2
-3
-3
-2
-2
-1
2
5
0
-5
-1
0
0
-3
-4
-2
6
0
-2
-2
-1
-4
-2
2
9
-5
-3
-2
0
7
-1
6
1
0
-6
-5
-1
3
1
-2
-3
-1
3
-5
-3
0
17
0
-6
10
2
4
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The BLAST algorithm
 Break the search sequence into words
• W = 3 for proteins, W = 12 for DNA
MCGPFILGTYC
CGP
MCG, CGP, GPF, PFI, FIL,
ILG, LGT, GTY, TYC
MCG
 Include in the search all words that score above
a certain value (T) for any search word
MCG
MCT
MCN
…
CGP
MGP
CTP
…
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…
This list can be
computed in linear
time
102
The Blast Algorithm (2)
 Search for the words in the database
• Word locations can be precomputed and indexed
• Searching for a short string in a long string

Regular expression matching: FSA
 HSP (High Scoring Pair) = A match between a
query word and the database
 Find a “hit”: Two non-overlapping HSP’s on a
diagonal within distance A
 Extend the hit until the score falls below a
threshold value, X
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OCCBIO 2006 – Fundamental Bioinformatics
104
Results from a BLAST search
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105
Search Significance Scores
 A search will always return some hits.
 How can we determine how “unusual” a
particular alignment score is?
• ORF’s

Assumptions
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106
Assessing significance requires a distribution
Frequency
 I have an apple of diameter 5”. Is that unusual?
Diameter (cm)
OCCBIO 2006 – Fundamental Bioinformatics
107
Is a match significant?
• Scoring system
• Database
• Sequence to search for
Length
 Composition

Frequency
 Match scores for aligning my sequence with
random sequences.
 Depends on:
Match score
 How do we determine the random sequences?
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108
Generating “random” sequences
 Random uniform model:
P(G) = P(A) = P(C) = P(T) = 0.25
• Doesn’t reflect nature
 Use sequences from a database
• Might have genuine homology

We want unrelated sequences
 Random shuffling of sequences
• Preserves composition
• Removes true homology
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109
What distribution do we expect to see?
 The mean of n random (i.i.d.) events tends
towards a Gaussian distribution.
• Example: Throw n dice and compute the mean.
• Distribution of means:
n=2
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n = 1000
110
The extreme value distribution
 This means that if we get the match scores for
our sequence with n other sequences, the mean
would follow a Gaussian distribution.
 The maximum of n (i.i.d.) random events tends
towards the extreme value distribution as n
grows large.
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Comparing distributions
Extreme Value:
Gaussian:

f x  
1


e
x

e
e

x 

OCCBIO 2006 – Fundamental Bioinformatics

1
f x  
e
 2
  x   2
2 2
112
Determining P-values
 If we can estimate  and , then we can
determine, for a given match score x, the
probability that a random match with score x or
greater would have occurred in the database.
 For sequence matches, a scoring system and
database can be parameterized by two
parameters, K and , related to  and .
• It would be nice if we could compare hit
significance without regard to the database and
scoring system used!
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113
Bit Scores
 The expected number of hits with score  S is:
E = Kmn e s
• Where m and n are the sequence lengths
 Normalize the raw score using:
S 
S  ln K
ln 2
 Obtains a “bit score” S’, with a standard set of
units.
S
 The new E-value is: E  mn 2
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P values and E values
 Blast reports E-values
 E = 5, E = 10 versus P = 0.993 and P = 0.99995
 When E < 0.01 P-values and E-values are
nearly identical
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115
BLAST parameters
 Lowering the neighborhood word threshold (T)
allows more distantly related sequences to be
found, at the expense of increased noise in the
results set.
 Raising the segment extension cutoff (X)
returns longer extensions for each hit.
 Changing the minimum E-value changes the
threshold for reporting a hit.
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Part V – Phylogenies
Preliminaries
Distance-based methods
Parsimony Methods
Phylogenetic Trees
 Hypothesis about the relationship between
organisms
 Can be rooted or unrooted
A
B
B
C
D
E
Time
A
E
C
D
Root
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118
Tree proliferation

2n  3!
N R  n2
2 n  2!
NU

2n  5!
 n 3
2 n  3!
Species Number of Rooted Trees
Number of Unrooted Trees
2
1
1
3
3
1
4
15
3
5
105
15
6
34,459,425
2,027,025
7
213,458,046,767,875
7,905,853,580,625
8
8,200,794,532,637,891,559,375
221,643,095,476,699,771,875
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Molecular phylogenetics
 Specific genomic
sequence variations
(alleles) are much
more reliable than
phenotypic
characteristics
 More than one gene
should be considered
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120
An ongoing didactic
 Pheneticists tend to prefer distance based
metrics, as they emphasize relationships among
data sets, rather than the paths they have taken
to arrive at their current states.
 Cladists are generally more interested in
evolutionary pathways, and tend to prefer more
evolutionarily based approaches such as
maximum parsimony.
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Distance matrix methods
Species
B
A
9
B
–
C
–
D
–
C
8
11
–
–
D
12
15
10
–
E
15
18
13
5
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122
UPGMA
 Similar to average-link clustering
 Merge the closest two groups
• Replace the distances for the new, merged group
with the average of the distance for the previous
two groups
 Repeat until all species are joined
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123
UPGMA Step 1
Species
B
A
9
B
–
C
–
D
–
C
8
11
–
–
D
12
15
10
–
E
15
18
13
5
Merge D & E
D
Species
B
A
9
B
–
C
–
C
8
11
–
DE
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E
13.5 16.5 11.5
124
UPGMA Step 2
Species
B
A
9
B
–
C
–
C
8
11
–
DE
Merge A & C
A
C
D
E
13.5 16.5 11.5
Species
AC
DE
OCCBIO 2006 – Fundamental Bioinformatics
B
10
AC
–
16.5 12.5
125
UPGMA Steps 3 & 4
Species
AC
DE
B
10
AC
–
Merge B & AC
A
C
B
D
E
16.5 12.5
Merge ABC & DE
A
C
B
D
E
(((A,C)B)(D,E))
OCCBIO 2006 – Fundamental Bioinformatics
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Parsimony approaches
 Belong to the broader class of character based
methods of phylogenetics
 Emphasize simpler, and thus more likely
evolutionary pathways
I: GCGGACG
II: GTGGACG
A
(C or T)
C
I
(C or T)
T
II
OCCBIO 2006 – Fundamental Bioinformatics
C
I
T
II
127
Informative and uninformative sites
Position
Seq 1
2
3
4
5
6
1
G
G
G
G
G
G
2
G
G
G
A
G
T
3
G
G
A
T
A
G
4
G
A
T
C
A
T
For positions 5 & 6, it is
possible to select more
parsimonious trees –
those that invoke less
substitutions.
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Parsimony methods
 Enumerate all possible trees
 Note the number of substitutions events
invoked by each possible tree
• Can be weighted by transition/transversion
probabilities, etc.
 Select the most parsimonious
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Branch and Bound methods
 Key problem – number of possible trees grows
enormous as the number of species gets large
 Branch and bound – a technique that allows
large numbers of candidate trees to be rapidly
disregarded
 Requires a “good guess” at the cost of the best
tree
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Branch and Bound for TSP
 Find a minimum cost
round-trip path that
visits each intermediate
city exactly once
 NP-complete
 Greedy approach:
A,G,E,F,B,D,C,A
= 251
OCCBIO 2006 – Fundamental Bioinformatics
A
93
20
D
82
B
59
31
57
12
G
17
C
46
82
35
E
68
F
15
131
Search all possible paths
A
93
20
All paths
D
82
B
59
31
57
12
G
17
C
46
82
35
AG (20)
E
68
F
AB (46)
AC (93)
15
AGF (88)
AGFB
AGFE
Best estimate: 251
OCCBIO 2006 – Fundamental Bioinformatics
AGE (55)
AGFC
ACB (175)
ACD
ACF
ACBE (257)

132
Parsimony – Branch and Bound
 Use the UPGMA tree for an initial best estimate
of the minimum cost (most parsimonious) tree
 Use branch and bound to explore all feasible
trees
 Replace the best estimate as better trees are
found
 Choose the most parsimonious
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Parsimony example
Position
Seq 1
2
3
4
5
6
1
G
G
G
G
G
G
2
G
G
G
A
G
T
3
G
G
A
T
A
G
4
G
A
T
C
A
T
Position 5:
All trees
(1,2) [0]
(1,3) [1]
(1,4) [1]
Etc.
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Part VI – Aligning protein sequences
PAM matrices
BLOSUM matrices
Sequence Alignments Revisited
 Scoring nucleotide sequence alignments was
easier
• Match score
• Possibly different scores for transitions and
transversions
 For amino acids, there are many more possible
substitutions
 How do we score which substitutions are highly
penalized and which are moderately penalized?
• Physical and chemical characteristics
• Empirical methods
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136
Scoring Mismatches
 Physical and chemical characteristics
• V  I – Both small, both hydrophobic,
conservative substitution, small penalty
• V  K – Small  large, hydrophobic  charged,
large penalty
• Requires some expert knowledge and judgement
 Empirical methods
• How often does the substitution V  I occur in
proteins that are known to be related?

Scoring matrices: PAM and BLOSUM
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137
PAM matrices
 PAM = “Point Accepted Mutation” interested
only in mutations that have been “accepted” by
natural selection
 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?
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138
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, cont’d
 Construct a phylogenetic tree for the sequences
in the alignment
ACGCTAFKI
AG
GCGCTAFKI
AG
GCGCTGFKI
FG,A = 3
IL
ACGCTAFKL
AL
GCGCTLFKI
CS
ASGCTAFKL
GA
ACACTAFKL
 Calculate substitution frequences FX,X
 Substitutions may have occurred either way, so
A  G also counts as G  A.
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Mutation Probabilities
 Mi,j represents the probability of J  I
substitution.
M ij 
m j Fij
ACGCTAFKI
 Fij
AG
GCGCTAFKI
i
AG
GCGCTGFKI
 M G, A
IL
ACGCTAFKL
AL
GCGCTLFKI
CS
ASGCTAFKL
GA
ACACTAFKL
2.7  3

= 2.025
4
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141
The PAM matrix
 The entries, Ri,j 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(2.025/0.1587) = log(12.760) = 1.106
 The log is taken so that we can add, rather than
multiply entries to get compound probabilities.
 Log-odds matrix
 Diagonal entries are 1– mj
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Interpretation of PAM matrices
 PAM-1 – one substitution per 100 residues (a
PAM unit of time)
 Multiply them together to get PAM-100, etc.
 “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’?”
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PAM matrix considerations
 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.
 PAM-1 – similar sequences, PAM-1000 very
dissimilar sequences
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BLOSUM matrix
 Starts by clustering proteins by similarity
 Avoids problems with small probabilities by
using averages over clusters
 Numbering works opposite
• BLOSUM-62 is appropriate for sequences of about
62% identity, while BLOSUM-80 is appropriate for
more similar sequences.
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Part VII – Protein Structure
Preliminaries
Lattice Models
Protein Folding Algorithms
Illustrations from: C Branden and J Tooze, Introduction to Protein Structure, 2 nd ed. Garland Pub. ISBN 0815302703
The many functions of proteins






Mechanoenzymes: myosin, actin
Rhodopsin: allows vision
Globins: transport oxygen
Antibodies: immune system
Enzymes: pepsin, renin, carboxypeptidase A
Receptors: transmit messages through
membranes
 Vitelogenin: molecular velcro
• And hundreds of thousands more…
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Proteins are chains of amino acids
 Polymer – a molecule composed of repeating units
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Amino acid composition
 Basic Amino Acid
Structure:
• The side chain, R,
varies for each of
the 20 amino acids
Side chain
R
H
N C C
H
Amino
group
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O
H
OH
Carboxyl
group
149
The Peptide Bond
 Dehydration synthesis
 Repeating backbone: N–C –C –N–C –C
O
O
• Convention – start at amino terminus and proceed
to carboxy terminus
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Peptidyl polymers
 A few amino acids in a chain are called a
polypeptide. A protein is usually composed of
50 to 400+ amino acids.
 Since part of the amino acid is lost during
dehydration synthesis, we call the units of a
protein amino acid residues.
carbonyl
carbon
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amide
nitrogen
151
Side chain properties
 Recall that the electronegativity of carbon is at
about the middle of the scale for light elements
• Carbon does not make hydrogen bonds with water
easily – hydrophobic
• O and N are generally more likely than C to h-bond
to water – hydrophilic
 We group the amino acids into three general
groups:
• Hydrophobic
• Charged (positive/basic & negative/acidic)
• Polar
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The Hydrophobic Amino Acids
Proline severely
limits allowable
conformations!
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The Charged Amino Acids
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The Polar Amino Acids
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More Polar Amino Acids
And then there’s…
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Planarity of the peptide bond
Psi () – the
angle of
rotation about
the C-C bond.
Phi () – the
angle of
rotation about
the N-C bond.
The planar bond angles and bond
lengths are fixed.
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Phi and psi
  =  = 180° is
extended
conformation
  : C to N–H
  : C=O to C
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C=O
C
N–H
158
The Ramachandran Plot
Observed
(non-glycine)
Calculated
Observed
(glycine)
 G. N. Ramachandran – first calculations of
sterically allowed regions of phi and psi
 Note the structural importance of glycine
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Primary & Secondary Structure
 Primary structure = the linear sequence of
amino acids comprising a protein:
AGVGTVPMTAYGNDIQYYGQVT…
 Secondary structure
• Regular patterns of hydrogen bonding in proteins
result in two patterns that emerge in nearly every
protein structure known: the -helix and the
-sheet
• The location of direction of these periodic,
repeating structures is known as the secondary
structure of the protein
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The alpha helix

 60°
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Properties of the alpha helix
     60°
 Hydrogen bonds
between C=O of
residue n, and
NH of residue
n+4
 3.6 residues/turn
 1.5 Å/residue rise
 100°/residue turn
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Properties of -helices
 4 – 40+ residues in length
 Often amphipathic or “dual-natured”
• Half hydrophobic and half hydrophilic
• Mostly when surface-exposed
 If we examine many -helices,
we find trends…
• Helix formers: Ala, Glu, Leu,
Met
• Helix breakers: Pro, Gly, Tyr,
Ser
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The beta strand (& sheet)
   135°
  +135°
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Properties of beta sheets
 Formed of stretches of 5-10 residues in
extended conformation
 Pleated – each C a bit
above or below the previous
 Parallel/aniparallel,
contiguous/non-contiguous
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Parallel and anti-parallel -sheets
 Anti-parallel is slightly energetically favored
Anti-parallel
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Parallel
166
Turns and Loops
 Secondary structure elements are connected by
regions of turns and loops
 Turns – short regions
of non-, non-
conformation
 Loops – larger stretches with no secondary
structure. Often disordered.
• “Random coil”
• Sequences vary much more than secondary
structure regions
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Levels of Protein
Structure
 Secondary structure
elements combine to
form tertiary structure
 Quaternary structure
occurs in multienzyme
complexes
• Many proteins are
active only as
homodimers,
homotetramers, etc.
Disulfide Bonds
 Two cyteines in
close proximity
will form a
covalent bond
 Disulfide bond,
disulfide bridge,
or dicysteine
bond.
 Significantly
stabilizes tertiary
structure.
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Protein Structure Examples
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Determining Protein Structure
 There are O(100,000) distinct proteins in the
human proteome.
 3D structures have been determined for 14,000
proteins, from all organisms
• Includes duplicates with different ligands bound,
etc.
 Coordinates are determined by X-ray
crystallography
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X-Ray Crystallography
~0.5mm
• The crystal is a mosaic of millions of copies
of the protein.
• As much as 70% is solvent (water)!
• May take months (and a “green” thumb) to
grow.
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X-Ray diffraction
 Image is averaged
over:
• Space (many copies)
• Time (of the diffraction
experiment)
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Electron Density Maps
 Resolution is
dependent on the
quality/regularity
of the crystal
 R-factor is a
measure of
“leftover” electron
density
 Solvent fitting
 Refinement
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The Protein Data Bank
 http://www.rcsb.org/pdb/
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
N
CA
C
O
CB
N
CA
C
O
N
CA
C
O
CB
CG1
CG2
ALA
ALA
ALA
ALA
ALA
GLY
GLY
GLY
GLY
VAL
VAL
VAL
VAL
VAL
VAL
VAL
E
E
E
E
E
E
E
E
E
E
E
E
E
E
E
E
1
1
1
1
1
2
2
2
2
3
3
3
3
3
3
3
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22.382
22.957
23.572
23.948
23.932
23.656
24.216
25.653
26.258
26.213
27.594
28.569
28.429
27.834
29.259
26.811
47.782
47.648
46.251
45.688
48.787
45.723
44.393
44.308
45.296
43.110
42.879
43.613
43.444
41.363
41.013
40.649
112.975
111.613
111.545
112.603
111.380
110.336
110.087
110.579
110.994
110.521
110.975
110.055
108.822
110.979
111.404
111.850
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
24.09
22.40
21.32
21.54
22.79
19.17
17.35
16.49
15.35
16.21
16.02
15.69
16.43
16.66
17.35
17.03
3APR
3APR
3APR
3APR
3APR
3APR
3APR
3APR
3APR
3APR
3APR
3APR
3APR
3APR
3APR
3APR
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
175
Views of a protein
Wireframe
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Ball and stick
176
Views of a protein
Spacefill
Cartoon
CPK colors
Carbon =
green, black,
or grey
Nitrogen =
blue
Oxygen = red
Sulfur =
yellow
Hydrogen =
white
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The Protein Folding Problem
 Central question of molecular biology:
“Given a particular sequence of amino acid
residues (primary structure), what will the
tertiary/quaternary structure of the resulting
protein be?”
 Input: AAVIKYGCAL…
Output: 11, 22…
= backbone conformation:
(no side chains yet)
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Forces driving protein folding
 It is believed that hydrophobic collapse is a key
driving force for protein folding
• Hydrophobic core
• Polar surface interacting with solvent




Minimum volume (no cavities)
Disulfide bond formation stabilizes
Hydrogen bonds
Polar and electrostatic interactions
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Folding help
 Proteins are, in fact, only marginally stable
• Native state is typically only 5 to 10 kcal/mole more
stable than the unfolded form
 Many proteins help in folding
• Protein disulfide isomerase – catalyzes shuffling of
disulfide bonds
• Chaperones – break up aggregates and (in theory)
unfold misfolded proteins
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The Hydrophobic Core
 Hemoglobin A is the protein in red blood cells
(erythrocytes) responsible for binding oxygen.
 The mutation E6V in the  chain places a
hydrophobic Val on the surface of hemoglobin
 The resulting “sticky patch” causes hemoglobin
S to agglutinate (stick together) and form fibers
which deform the red blood cell and do not
carry oxygen efficiently
 Sickle cell anemia was the first identified
molecular disease
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Sickle Cell Anemia
Sequestering hydrophobic residues in
the protein core protects proteins from
hydrophobic agglutination.
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Computational Problems in Protein Folding
 Two key questions:
• Evaluation – how can we tell a correctly-folded
protein from an incorrectly folded protein?
H-bonds, electrostatics, hydrophobic effect, etc.
 Derive a function, see how well it does on “real” proteins

• Optimization – once we get an evaluation function,
can we optimize it?
Simulated annealing/monte carlo
 EC
 Heuristics
 We’ll talk more about these methods later…

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Fold Optimization
 Simple lattice models (HPmodels)
• Two types of residues:
hydrophobic and polar
• 2-D or 3-D lattice
• The only force is hydrophobic
collapse
• Score = number of HH
contacts
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Scoring Lattice Models
 H/P model scoring: count noncovalent
hydrophobic interactions.
 Sometimes:
• Penalize for buried polar or surface hydrophobic
residues
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What can we do with lattice models?
 For smaller polypeptides, exhaustive search can
be used
• Looking at the “best” fold, even in such a simple
model, can teach us interesting things about the
protein folding process
 For larger chains, other optimization and search
methods must be used
• Greedy, branch and bound
• Evolutionary computing, simulated annealing
• Graph theoretical methods
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Learning from Lattice Models
 The “hydrophobic zipper” effect:
Ken Dill ~ 1997
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Representing a lattice model
 Absolute directions
• UURRDLDRRU
 Relative directions
• LFRFRRLLFFL
• Advantage, we can’t have UD or RL in absolute
• Only three directions: LRF
 What about bumps? LFRRR
• Bad score
• Use a better representation
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Preference-order representation
 Each position has two “preferences”
• If it can’t have either of the two, it will take the
“least favorite” path if possible
 Example: {LR},{FL},{RL},
{FR},{RL},{RL},{FR},{RF}
 Can still cause bumps:
{LF},{FR},{RL},{FL},
{RL},{FL},{RF},{RL},
{FL}
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More realistic models
 Higher resolution lattices (45° lattice, etc.)
 Off-lattice models
• Local moves
• Optimization/search methods and /
representations
Greedy search
 Branch and bound
 EC, Monte Carlo, simulated annealing, etc.

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The Other Half of the Picture
 Now that we have a more realistic off-lattice
model, we need a better energy function to
evaluate a conformation (fold).
 Theoretical force field:
• G = Gvan der Waals + Gh-bonds + Gsolvent +
Gcoulomb
 Empirical force fields
• Start with a database
• Look at neighboring residues – similar to known
protein folds?
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Threading: Fold recognition
 Given:
• Sequence:
IVACIVSTEYDVMKAAR…
• A database of molecular
coordinates
 Map the sequence onto
each fold
 Evaluate
• Objective 1: improve
scoring function
• Objective 2: folding
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Secondary Structure Prediction
AGVGTVPMTAYGNDIQYYGQVT…
A-VGIVPM-AYGQDIQY-GQVT…
AG-GIIP--AYGNELQ--GQVT…
AGVCTVPMTA---ELQYYG--T…
AGVGTVPMTAYGNDIQYYGQVT…
----hhhHHHHHHhhh--eeEE…
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Secondary Structure Prediction

Easier than folding
•

Current algorithms can prediction secondary
structure with 70-80% accuracy
Chou, P.Y. & Fasman, G.D. (1974).
Biochemistry, 13, 211-222.
•

Based on frequencies of occurrence of residues in
helices and sheets
PhD – Neural network based
•
•
Uses a multiple sequence alignment
Rost & Sander, Proteins, 1994 , 19, 55-72
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Chou-Fasman Parameters
Name
Alanine
Arginine
Aspartic Acid
Asparagine
Cysteine
Glutamic Acid
Glutamine
Glycine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Proline
Serine
Threonine
Tryptophan
Tyrosine
Valine
Abbrv
A
R
D
N
C
E
Q
G
H
I
L
K
M
F
P
S
T
W
Y
V
P(a)
142
98
101
67
70
151
111
57
100
108
121
114
145
113
57
77
83
108
69
106
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P(b) P(turn)
83
66
93
95
54
146
89
156
119
119
37
74
110
98
75
156
87
95
160
47
130
59
74
101
105
60
138
60
55
152
75
143
119
96
137
96
147
114
170
50
f(i)
0.06
0.07
0.147
0.161
0.149
0.056
0.074
0.102
0.14
0.043
0.061
0.055
0.068
0.059
0.102
0.12
0.086
0.077
0.082
0.062
f(i+1)
0.076
0.106
0.11
0.083
0.05
0.06
0.098
0.085
0.047
0.034
0.025
0.115
0.082
0.041
0.301
0.139
0.108
0.013
0.065
0.048
f(i+2)
0.035
0.099
0.179
0.191
0.117
0.077
0.037
0.19
0.093
0.013
0.036
0.072
0.014
0.065
0.034
0.125
0.065
0.064
0.114
0.028
f(i+3)
0.058
0.085
0.081
0.091
0.128
0.064
0.098
0.152
0.054
0.056
0.07
0.095
0.055
0.065
0.068
0.106
0.079
0.167
0.125
0.053
195
Chou-Fasman Algorithm
 Identify -helices
• 4 out of 6 contiguous amino acids that have P(a) >
100
• Extend the region until 4 amino acids with P(a) <
100 found
• Compute P(a) and P(b); If the region is >5
residues and P(a) > P(b) identify as a helix
 Repeat for -sheets [use P(b)]
 If an  and a  region overlap, the overlapping
region is predicted according to P(a) and
P(b)
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Chou-Fasman, cont’d
 Identify hairpin turns:
• P(t) = f(i) of the residue  f(i+1) of the next residue
 f(i+2) of the following residue  f(i+3) of the
residue at position (i+3)
• Predict a hairpin turn starting at positions where:
P(t) > 0.000075
 The average P(turn) for the four residues > 100
 P(a) < P(turn) > P(b) for the four residues

 Accuracy  60-65%
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Chou-Fasman Example
 CAENKLDHVRGPTCILFMTWYNDGP
 CAENKL – Potential helix (!C and !N)

Residues with P(a) < 100: RNCGPSTY
• Extend: When we reach RGPT, we must stop
• CAENKLDHV: P(a) = 972, P(b) = 843
• Declare alpha helix
 Identifying a hairpin turn
• VRGP: P(t) = 0.000085
• Average P(turn) = 113.25

Avg P(a) = 79.5, Avg P(b) = 98.25
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Other topics?
 Tools and languages
 Forensic DNA
 Microarray analysis
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