1. Find the replication origins in Genomics

2. Herpesvirus Members of the family herpesviridae are found in a wide range of host systems.

3. Feature of Herpesvirus Herpesviruses utilize two types of replication origins during lytic and latent infection. For each type of origins, the count and locations in genome vary from one kind of herpesvirus to another. Most herviruses have one to twp copies of latent and lytic origins.

4. Understanding the molecular mechanisms involved in DNA replication is of great importance in further developing strategies to control the growth and spread of viruses..

5. Replication origins of Herpesvirus Many studies have reported that nucleotide sequences around replication origins of certain herpesvirus have complex repetitive structures of closely spaced direct and inverted repeats. A high concentration of palindromes around replication origins has been found in herpesviruses. origins repeat

6. Palindrome A palindrome is a special case of inverted repeats where a segment of nucleotide bases is immediately followed by its reverse complement. 5’ ….. GCAATATTGC ….. 3’ 3’ ….. CGTTATAACG ….. 5’ Palindromes play important roles as protein-binding sites in DNA replication processes.

7. Methods for predicting replication origins. David S.H. Chew, …(NAR., 2005) Our method.

8. Step of David’ method (i) Locate palindromes at or above a prescribed length. -> L (ii) choose a scoring scheme for palindromes. (iii) compute a score for fixed slice window of the genome according to the chosen scoring scheme. (iv) select regions with high scores.

9. Shift with half size of Slice window window palindrome Window score = sum of score of palindormes

10. Scoring scheme for palindromes (i) Palindrome count score (PCS): In this scoring scheme, a palindrome is given a score 1 when its length is at or above 2L. (ii) Palindrome length score (PLS): A palindrome of length 2s >= 2L is given a score s/L. (iii) Base-pair weighted score of order m (BWS m ). Base on markov type sequence models. m denote the order of markov chain.

11. Computing the window score The score of windows is sum of palindrome’s score within.

12. Step of Our method (i) Locate palindromes at or above a prescribed length. -> L (ii) choose a scoring scheme for palindromes. (iii) compute a score for random slice window of the genome according to the chosen scoring scheme. (iv) select regions with high scores.

13. Random slice window Give a range of size of windows. palindrome

14. Computing the window score

15. Results Fixed slice window give the size of 500. Range of random window is 100 -> 1000.

16. Demo http://www.stat.sinica.edu.tw/palindrome