Longest Common Subsequence LCS Scoring

1
Longest Common Subsequence (LCS) - Scoring

• Dr. Nancy Warter-Perez
• June 25, 2003

2
Hydrophobicity Sliding Window Program Using
Functions (1)

• include ltiostreamgt
• include ltstringgt
• using namespace std
• double hydro25 1.8,0,2.5,-3.5,-3.5,2.8,-0.4,-
  3.2,4.5,0,-3.9,3.8,1.9,-3.5,0,
• -1.6,-3.5,-4.5,-0.8,-0.7,0,4.2,-0.9,0,-1.3
• void compute_hydro(string seq, int ws)
• void main ()
• string seq int ws
• cout ltlt "This program will compute the
  hydrophobicity of an sequence of amino acids.\n
• cout ltlt "Please enter the sequence "ltlt
  flush cin gtgt seq
• cout ltlt "Please enter the window size "ltlt
  flush cin gtgt ws
• compute_hydro(seq, ws)

3
Hydrophobicity Sliding Window Program Using
Functions (2)

• void compute_hydro(string seq, int ws)
• int i double sum 0
• cout ltlt "\n\nThe hydrophocity values are" ltlt
  endl
• for(i 0 i lt seq.size() i)
• if((seq.data()i gt 'a') (seq.data()i
  lt 'z'))
• seq.at(i) seq.data()i - 32
• for(i 0 i lt ws i)
• sum hydroseq.data()i - 'A'
• for(i 1 i lt seq.size() - ws i)
• cout ltlt "Hydrophocity value\t" ltlt sum/ws
  ltlt endl
• sum sum - hydroseq.data()i-1 - 'A'
  hydroseq.data()iws-1 - 'A'
• cout ltlt "Hydrophocity value\t" ltlt sum/ws ltlt
  endl

4
Reference

• Computational Molecular Biology An Algorithmic
  Approach, Pavel Pevzner

5
Longest Common Subsequence (LCS) Problem

• Can have insertion and deletions but no
  substitutions (no mismatches)
• Ex V ATCTGAT
• W TGCATA
• LCS TCTA

6
LCS Problem (cont.)

• Similarity score
• si-1,j
• si,j max si,j-1
• si-1,j-1 1, if vi wj
• On board example Pevzner Fig 6.1

7
Indels insertions and deletions (e.g., gaps)

• alignment of V and W
• V rows of similarity matrix (vertical axis)
• W columns of similarity matrix (horizontal
  axis)
• Space (gap) in W ? (UP)
• insertion
• Space (gap) in V ? (LEFT)
• deletion
• Match (no mismatch in LCS) (DIAG)

8
LCS(V,W) Algorithm

• for i 1 to n
• si,0 0
• for j 1 to n
• s0,j 0
• for i 1 to n
• for j 1 to m
• if vi wj
• si,j si-1,j-1 1 bi,j DIAG
• else if si-1,j gt si,j-1
• si,j si-1,j bi,j UP
• else
• si,j si,j-1 bi,j LEFT

9
Programming Workshop 5

• Implement the LCS scoring algorithm as a function
• Inputs 2 strings to score
• Outputs Scoring matrix and traceback matrix
  (these can be global variables)
• Write a main functions to
• prompt the user for 2 sequences
• call the scoring function
• print the 2 matrices