Bioinformatický seminár

Tue 24 Feb. 2009, 17:20

Title: Kahn and Raphael (2009) A Parsimony Approach to Analysis of Human Segmental Duplications.
Speaker: Michal Burger

Budeme diskutovať o článku

Crystal L. Kahn, Benjamin J. Raphael. A Parsimony Approach to Analysis of
Human Segmental Duplications. In Pacific Symposium on Biocomputing 
(PSB 2009), 2009.

Segmental duplications are abundant in the human genome, but their evolutionary
history is not well-understood. The mystery surrounding them is due in part to
their complex organization; many segmental duplications are mosaic patterns of
smaller repeated segments, or duplicons. A two-step model of duplication has been
proposed to explain these mosaic patterns. In this model, duplicons are copied and
aggregated into primary duplication blocks that subsequently seed secondary duplications.
Here, we formalize the problem of computing a duplication scenario
that is consistent with the two-step model. We first describe a dynamic programming
algorithm to compute the duplication distance between two strings. We then
use this distance as the cost function in an integer linear program to obtain the
most parsimonious duplication scenario. We apply our method to derive putative
ancestral relationships between segmental duplications in the human genome.