1. . Sequence Alignment Author:- Aya Osama Supervision:- Dr.Noha khalifa

2. Sequence Alignment Variants variants of sequence alignment: u Global alignment (The Needelman-Wunsch Algorithm) u Local alignment (The Smith-Waterman Algorithm) u Blast Alignment(basic local alignment tool) 2

3. Global Sequence Alignment u It is an example of dynamic programming, and was the first application of dynamic programming to biological sequence comparisondynamic programming u Suitable when the two sequences are of similar length, with a significant degree of similarity throughout 3

4. Local Sequence Alignment u Useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context 4

5. 5 Sequence Comparison Much of bioinformatics involves sequences u DNA sequences u RNA sequences u Protein sequences We can think of these sequences as strings of letters u DNA & RNA: |alphabet|=4 u Protein: |alphabet|=20

6. 6 Global Alignment Input: two sequences over the same alphabet Output: an alignment of the two sequences Example: u GCGCATGGATTGAGCGA and TGCGCCATTGATGACCA u A possible alignment: -GCGC-ATGGATTGAGCGA TGCGCCATTGAT-GACC-A

7. 7 -GCGC-ATGGATTGAGCGA TGCGCCATTGAT-GACC-A Three elements: u Perfect matches u Mismatches u Insertions & deletions (indel) Global Alignment Example (cont): Symmetric view of evolution

8. 8 Score each position independently: u Match: +1 u Mismatch: -1 u Indel: -2 Score of an alignment is sum of position scores Global Alignment scoring scheme Example: -GCGC-ATGGATTGAGCGA TGCGCCATTGAT-GACC-A Score: (+1x13) + (-1x2) + (-2x4) = 3 ------GCGCATGGATTGAGCGA TGCGCC----ATTGATGACCA-- Score: (+1x5) + (-1x6) + (-2x11) = -23

9. How to make alignment between two sequences? 9

10. How to make alignment between two sequences?(cont’d) 10

11. How to make alignment between two sequences?(cont’d) 11

12. How to make alignment between two sequences?(cont’d) 12

13. How to make alignment between two sequences?(cont’d) 13

14. How to make alignment between two sequences?(cont’d) 14

15. How to make alignment between two sequences?(cont’d) 15

16. Refrences www.wikipedia.com http://seqtool.sdsc.edu/CGI/B W.cgi#! 16

17. Thanks Any Questions?? 17