Sequence Alignment I Lecture

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Sequence 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.
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Sequence 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,)

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Sequence 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

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Sequence 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

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Alignments

• -GCGC-ATGGATTGAGCGA
• TGCGCCATTGAT-GACC-A
• Three components
• Perfect matches
• Mismatches
• Insertions deletions (indel)

Formal definition of alignment
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Choosing Alignments

• There are many (how many?) possible alignments
• For example, compare
• -GCGC-ATGGATTGAGCGA
• TGCGCCATTGAT-GACC-A
• to
• ------GCGCATGGATTGAGCGA
• TGCGCC----ATTGATGACCA--
• Which one is better?

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Scoring 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

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A Naive Scoring Rule

• Each position scored independently, using
• Match 1
• Mismatch -1
• Indel -2
• Score of an alignment is sum of position scores

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Example

• -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

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More 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 ?

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Additive 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

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The 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.

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Computing 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.

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Recursive 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 )

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Recursive 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 )

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Recursive 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 )

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Useful Notation

• (ab)use of notation
• Vi,j value of optimal alignment between
• i prefix of s and j prefix of t.

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Recursive 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

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Recursive Argument

• Of course, we also need to handle the base cases
  in the recursion (boundary of matrix)

AA - -
versus
We fill the interior of matrix using our
recurrence rule
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Dynamic Programming Algorithm
We continue to fill the matrix using the
recurrence rule
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Dynamic Programming Algorithm
versus
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Dynamic Programming Algorithm
(hey, what is the scoring function s(x,y) ? )
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Dynamic Programming Algorithm
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Reconstructing the Best Alignment

• To reconstruct the best alignment, we record
  which case(s) in the recursive rule maximized the
  score

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Reconstructing the Best Alignment

• We now trace back a path that corresponds to the
  best alignment

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Reconstructing the Best Alignment

• More than one alignment could have the best score
• (sometimes, even exponentially many)

AAAC A-GC
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Time Complexity

• Space O(mn)
• Time O(mn)
• Filling the matrix O(mn)
• Backtrace O(mn)

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Space Complexity

• In real-life applications, n and m can be very
  large
• The space requirements of O(mn) can be too
  demanding
• If m n 1000, we need 1MB space
• If m n 10000, we need 100MB 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?

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Why 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 requires keeping all back
  pointers, O(mn) memory.

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Local 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.

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Local 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.

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Local 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).

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Local Alignment

• New option
• We can start a new match instead of extending a
  previous alignment

Alignment of empty suffixes
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Local Alignment Example
s TAATA t TACTAA
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Local Alignment Example
s TAATA t TACTAA
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Local Alignment Example
s TAATA t TACTAA