#### Transcript Multiple Alignment and Phylogenetic Trees

```Multiple Alignment and
Phylogenetic Trees
Csc 487/687 Computing for
Bioinformatics
Alignment problem
Given a set of sequences, produce a
multiple alignment which corresponds as
well as possible to the biological
relationships between the corresponding
bio-molecules
For homologous proteins

Two residues should be aligned (on top of
each other)


if they are homologous (evolved from the
same residue in a common ancestor protein)
if they are structurally equivalent
Automatic approach

Need a way of scoring alignments

fitness function which for an alignment
quantifies its “goodness”

Need an algorithm for finding alignments
with good scores

Not all methods provide a scoring function
for the final alignment!
Analysis of fitness function

One can test whether the alignments
optimal under a given fitness function
correspond well to the biological
relationships between the sequences

For example, if the structure of (some of)
the proteins are known.
Scoring Alignments

In order to find an optimal alignment, we
need to be able to measure how good an
alignment is


Sum of pairs (SP) method: in a column, score
each pair of letters and total the scores. Pairs
of gaps score 0.
Total up scores for each column
SP Method Example
S
S
I
I
S
K
K
E


Using BLOSUM62 matrix,
gap penalty -8
In column 1, we have pairs



-8 - 8 + 4 = -12

-,S
-,S
S,S
k(k-1)/2 pairs per column
Align by use of dynamic programming

Dynamic programming finds best alignment of
k sequences with given scoring scheme

For two sequences there are three different
column types

For three sequences there are seven different
column types
x means an amino acid, - a blank
Sequence1
x - x x - - x
Sequence2
x x - x - x Sequence3
x x x - x - x
Use of dynamic programming

Dynamic programming finds best
alignment of k sequences given
scoring scheme
Algorithm for dynamic programming
Analysis
O(nk) entries to fill
 Each entry combines O(2k) other entries
 Costs O(k2) to calculate each SP score
 Overall cost is O(k2 2k nk), or exponential
in the number of sequences!
 NP-complete

General progressive alignment
Algorithm. General progressive alignment.
Progressive alignment of the sequences {s1, s2, . . . , sm}
Var C
current set of alignments
begin
C := ∅
for i := 1 to m do C := C union {{si }} end one alignment of
each seq.
for i := 1 to m − 1 do
choose two alignments Ap,Aq from C; C := C − {Ap,Aq }
Ar := align(Ap,Aq );C := C union {Ar }
end
C now contains the (single) final alignment
end
The Clustal Algorithm

Three steps:
1
2
3
Compare all pairs of sequences to obtain a
similarity matrix
Based on the similarity matrix, make a guide
tree relating all the sequences
Perform progressive alignment where the order
of the alignments is determined by the guide
tree
(A)
1 pairwise comparison
2 clustering/making tree
(B)
3 Align according to tree
Clustal - summary
Does not use a score for the final
alignment
 Each pairwise alignment is done using
dynamic programming
 Heuristics are used - tailored to globular
proteins
 Graphical version: ClustalX

Phylogeny

The basic principle is that the origin of
similarity is common ancestry.

The field of phylogeny has the goals of
working out the relationships among
species, populations, individuals, or genes.

Usually expressed as a tree.
Phylogeny

The basic principle is that the origin of
similarity is common ancestry.

The field of phylogeny has the goals of
working out the relationships among
species, populations, individuals, or genes.

Usually expressed as a tree.
Phylogeny

A statement of phylogeny among objects
assumes homology and depends on
classification.

Phylogeny states a topology of the
relationships based on classification
according to similarity of one or more sets
of characters, or on a model of
evolutionary processes.
Phylogeny

It is rare for species relationships and
ancestry to be directly observable.

Evolutionary trees determined from
genetic data are often based on inferences
from the patterns of similarity, which are
all that is observable among species living
now.
```