Pairwise Sequence Alignment (I) (Lecture for CS498-CXZ Algorithms in Bioinformatics) Sept. 22, 2005 ChengXiang Zhai Department of Computer Science University of Illinois, Urbana-Champaign Many slides are taken/adapted from http:// www.bioalgorithms.info/slides.htm
Pairwise Sequence Alignment (I). (Lecture for CS498-CXZ Algorithms in Bioinformatics) Sept. 22, 2005 ChengXiang Zhai Department of Computer Science University of Illinois, Urbana-Champaign. Many slides are taken/adapted from http://www.bioalgorithms.info/slides.htm. - PowerPoint PPT Presentation
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Pairwise Sequence Alignment (I)
(Lecture for CS498-CXZ Algorithms in Bioinformatics)
Sept. 22, 2005
ChengXiang Zhai
Department of Computer Science
University of Illinois, Urbana-Champaign
Many slides are taken/adapted from http://www.bioalgorithms.info/slides.htm
• Small islands of similarity corresponding to similarities between exons
• Such comparisons are quite common in biology research
Alignment of sequences is one of the most basic and most important problems in bioinformatics…
Outline
• Defining the problem of alignment
• The longest common subsequence problem
• Dynamic programming algorithms for alignment
Aligning Two Strings
Given the strings:
• v = ATGTTAT
• w = ATCGTAC
One possible alignment of the strings:
AT_GTTAT_
ATCGT_A_C
1st row – string v with with space symbols “-” inserted
2nd row – string w with with space symbols “-” inserted
Aligning Two Strings (cont’d)
Another way to represent each row shows the number of symbols of the sequence present up to a given position. For example the above sequences can be represented as:
0 1 2 2 3 4 5 6 7 7
0 1 2 3 4 5 5 6 6 7
AT_GTTAT_ ATCGT_A_C
Alignment Matrix
Both rows of the alignment can be represented in the resulting matrix:
0 1 2 2 3 4 5 6 7 7
0 1 2 3 4 5 5 6 6 7
AT_GTTAT_ ATCGT_A_C
0 1 2 2 3 4 5 6 7 7
0 1 2 3 4 5 5 6 6 7
Alignment as a Path in the Edit Graph
0 0 1 1 2 2 3 4 5 6 7 72 2 3 4 5 6 7 7 A A T _ G T T A T _T _ G T T A T _ A A T C G T _ A _ CT C G T _ A _ C0 0 1 1 2 3 4 5 5 6 6 7 2 3 4 5 5 6 6 7
(0,0) , (0,0) , (1,1)(1,1)
Alignment as a Path in the Edit Graph
0 1 0 1 2 2 2 3 4 5 6 7 72 3 4 5 6 7 7 A A T T _ G T T A T __ G T T A T _ A A T T C G T _ A _ CC G T _ A _ C0 1 0 1 2 2 3 4 5 5 6 6 7 3 4 5 5 6 6 7
(0,0) , (1,1) , (0,0) , (1,1) , (2,2)(2,2)
Alignment as a Path in the Edit Graph
0 1 2 2 0 1 2 2 33 4 5 6 7 7 4 5 6 7 7 A T _ A T _ G G T T A T _T T A T _ A T C A T C G G T _ A _ CT _ A _ C0 1 2 3 0 1 2 3 4 4 5 5 6 6 7 5 5 6 6 7