1. CSE-700 Parallel Programming Assignment 6 POSTECH Oct 19, 2007 박성우

2. 2 Species and Sequences Sequence 1 Species Sequence 2 Sequence n...

3. 3 Ortholog Last Common Ancestor S Human S1 Dog S2 By speciation

4. 4 Paralog Human S S1S1' By duplication

5. 5 Inparalog Last Common Ancestor S Human S1 Chimpanzee S2 By speciation S1' By duplication

6. 6 Paralog - Outparalog LCA HumanDog LCA = Last Common Ancestor SS'S1S1'S2S2'

7. 7 Coortholog S1' Species A S1 Species B S2 S2'

8. 8 Input Assume a total of n species S1, S2,..., Sn For each pair of species {Si, Sj} –Ortholog and paralog relations Thus n(n + 1)/2 ortholog/paralog files

9. 9 Seed Ortholog Species A Si Species B Sj 1.0 Cluster

10. 10 Invariant: No Two Seed Orthologs for Any Sequence Species A Si Species B Sj 1.0 Sk 1.0

11. 11 Ortholog and Paralogs Species A Si Species B Sj 1.0 Cluster Si'

12. 12 Output Assume a total of n species S1, S2,..., Sn Ortholog and paralog relations among all these species In each cluster, –seed ortholog from each pair of species –paralogs may be included.

13. 13 Example of Cluster [1] A S1'S1 B S2S2' C S3S3' D S4'S4

14. 14 Example of Cluster [2] A S1'S1 B S2S2' C S3S3' D S4'S4

15. 15 Bad Clusters [1] A S1'S1 B S2S2' C S3S3' D S4'S4 E S5'S5

16. 16 Bad Clusters [2] C S3 D S4'S4 E S6'S6 S4'' S5

17. 17 Input File Format Each line consists of: –Cluster number –Similarity score –Species name –Seed ortholog –Sequence name

18. 18 Goal Implement ANY sequential algorithm –There is no definitive answer. Then parallelize it. A parser and an output module are provided. –no string comparion –all integer operations