Title: Sequence Alignment I Lecture
1Sequence Alignment ILecture 2
Background Readings Gusfield, chapter 11.
Durbin et. al.,
chapter 2.
This class has been edited from Nir Friedmans
lecture which is available at www.cs.huji.ac.il/n
ir. Changes made by Dan Geiger, then Shlomo
Moran, and finally Benny Chor.
2Sequence Comparison
- Much of bioinformatics involves sequences
- DNA sequences
- RNA sequences
- Protein sequences
- We can think of these sequences as strings of
letters - DNA RNA alphabet ? of 4 letters (A,C,T/U,G)
- Protein alphabet ? of 20 letters (A,R,N,D,C,Q,)
3Sequence Comparison (cont)
- Finding similarity between sequences is important
for many biological questions - For example
- Find similar proteins
- Allows to predict function structure
- Locate similar subsequences in DNA
- Allows to identify (e.g) regulatory elements
- Locate DNA sequences that might overlap
- Helps in sequence assembly
4Sequence Alignment
- Input two sequences over the same alphabet
- Output an alignment of the two sequences
- Example
- GCGCATGGATTGAGCGA
- TGCGCCATTGATGACCA
- A possible alignment
- -GCGC-ATGGATTGAGCGA
- TGCGCCATTGAT-GACC-A
5Alignments
- -GCGC-ATGGATTGAGCGA
- TGCGCCATTGAT-GACC-A
- Three components
- Perfect matches
- Mismatches
- Insertions deletions (indel)
Formal definition of alignment
6Choosing Alignments
- There are many (how many?) possible alignments
- For example, compare
- -GCGC-ATGGATTGAGCGA
- TGCGCCATTGAT-GACC-A
- to
- ------GCGCATGGATTGAGCGA
- TGCGCC----ATTGATGACCA--
- Which one is better?
7Scoring Alignments
- Motivation
- Similar (homologous) sequences evolved from a
common ancestor - In the course of evolution, the sequences changed
from the ancestral sequence by random mutations - Replacements one letter changed to another
- Deletion deletion of a letter
- Insertion insertion of a letter
- Scoring of sequence similarity should reflect how
many and which operations took place
8A Naive Scoring Rule
- Each position scored independently, using
- Match 1
- Mismatch -1
- Indel -2
- Score of an alignment is sum of position scores
9Example
- -GCGC-ATGGATTGAGCGA
- TGCGCCATTGAT-GACC-A
- Score (1x13) (-1x2) (-2x4) 3
- ------GCGCATGGATTGAGCGA
- TGCGCC----ATTGATGACCA--
- Score (1x5) (-1x6) (-2x11) -23
- according to this scoring, first alignment is
better
10More General Scores
- The choice of 1,-1, and -2 scores is quite
arbitrary - Depending on the context, some changes are more
plausible than others - Exchange of an amino-acid by one with
- similar properties (size, charge, etc.)
- vs.
- Exchange of an amino-acid by one with very
different properties - Probabilistic interpretation (e.g.) How likely
is one alignment versus another ?
11Additive Scoring Rules
- We define a scoring function by specifying
- ?(x,y) is the score of replacing x by y
- ?(x,-) is the score of deleting x
- ?(-,x) is the score of inserting x
- The score of an alignment is defined as the
- sum of position scores
12The Optimal Score
- The optimal (maximal) score between two sequences
is the maximal score of all alignments of these
sequences, namely, - Computing the maximal score or actually finding
an alignment that yields the maximal score are
closely related tasks with similar algorithms. - We now address these problems.
13Computing Optimal Score
- How can we compute the optimal score ?
- If s n and t m, the number A(m,n) of
possible alignments is large! - Exercise Show that
- So it is not a good idea to go over all
alignments - The additive form of the score allows us to apply
dynamic programming to compute optimal score
efficiently.
14Recursive Argument
- Suppose we have two sequencess1..n1 and
t1..m1 - The best alignment must be one of three cases
- 1. Last match is (sn1,tm 1 )
- 2. Last match is (sn 1,-)
- 3. Last match is (-, tm 1 )
15Recursive Argument
- Suppose we have two sequencess1..n1 and
t1..m1 - The best alignment must be one of three cases
- 1. Last match is (sn1,tm 1 )
- 2. Last match is (sn 1,-)
- 3. Last match is (-, tm 1 )
16Recursive Argument
- Suppose we have two sequencess1..n1 and
t1..m1 - The best alignment must be one of three cases
- 1. Last match is (sn1,tm 1 )
- 2. Last match is (sn 1,-)
- 3. Last match is (-, tm 1 )
17Useful Notation
- (ab)use of notation
- Vi,j value of optimal alignment between
- i prefix of s and j prefix of t.
18Recursive Argument
- (ab)use of notation
- Vi,j value of optimal alignment between
- i prefix of s and j prefix of t.
- Using our recursive argument, we get the
following recurrence for V
19Recursive Argument
- Of course, we also need to handle the base cases
in the recursion (boundary of matrix)
AA - -
vs.
We fill the interior of matrix using our
recurrence rule
20Dynamic Programming Algorithm
We continue to fill the matrix using the
recurrence rule
21Dynamic Programming Algorithm
versus
22Dynamic Programming Algorithm
(hey, what is the scoring function s(x,y) ? )
23Dynamic Programming Algorithm
24Reconstructing the Best Alignment
- To reconstruct the best alignment, we record
which case(s) in the recursive rule maximized the
score
25Reconstructing the Best Alignment
- We now trace back a path that corresponds to the
best alignment
26Reconstructing the Best Alignment
- More than one alignment could have the best score
- (sometimes, even exponentially many)
AAAC A-GC
27Time Complexity
- Space O(mn)
- Time O(mn)
- Filling the matrix O(mn)
- Backtrace O(mn)
28Space Complexity
- In real-life applications, n and m can be very
large - The space requirements of O(mn) can be fairly
demanding - If m n 10,000, we need 100MB space
- If m n 100,000, we need 10GB space
- We can afford to perform extra computation to
save space - Looping over million operations takes less than
seconds on modern workstations - Can we trade space with time?
29Why Do We Need So Much Space?
To compute just the value Vn,mV(s1..n,t1..m
), we need only O(min(n,m)) space
- Compute V(i,j), column by column, storing only
two columns in memory - (or line by line if lines are shorter).
- Note however that
- This trick fails if we want to reconstruct the
optimal alignment. - Trace back information seemingly
- requires keeping all back pointers, O(mn)
memory. - Will get back to this.
30Local Alignment
- The alignment version we studies so far is called
- global alignment We align the whole sequence s
- to the whole sequence
t. - Global alignment is appropriate when s,t are
highly - similar (examples?), but makes little sense if
they - are highly dissimilar. For example, when s (the
query) - is very short, but t (the database) is very
long.
31Local Alignment
- When s and t are not necessarily similar, we may
want to consider a different question - Find similar subsequences of s and t
- Formally, given s1..n and t1..m find i,j,k,
and l such that V(si..j,tk..l) is maximal - This version is called local alignment.
32Local Alignment
- As before, we use dynamic programming
- We now want to setVi,j to record the maximum
value over all alignments of a suffix of s1..i - and a suffix of t1..j
- In other words, we look for a suffix of a
prefix. - How should we change the recurrence rule?
- Same as before but with an option to start afresh
- The result is called the Smith-Waterman
algorithm, after its inventors (1981).
33Local Alignment
- New option
- We can start a new match instead of extending a
previous alignment
Alignment of empty suffixes
34Local Alignment Example
s TAATA t TACTAA
35Local Alignment Example
s TAATA t TACTAA
36Local Alignment Example
s TAATA t TACTAA
What score should we take? 1 (lower right
corner) 3 (max) or something else?
37Local Alignment Example
s TAATA t TACTAA
38Local Alignment Example
s TAATA t TACTAA