A PARSIMONY APPROACH TO ANALYSIS OF HUMAN SEGMENTAL DUPLICATIONS

被引：0

作者：

Kahn, Crystal L. ^{[1
]}

Raphael, Benjamin J. ^{[2
]}

机构：

[1] Brown Univ, Dept Comp Sci, Box 1910, Providence, RI 02912 USA

[2] Brown Univ, Ctr Comput Molecul Bio, Box 1910, Providence, RI 02912 USA

来源：

PACIFIC SYMPOSIUM ON BIOCOMPUTING 2009 | 2009年

基金：

美国国家科学基金会;

关键词：

TANDEMLY REPEATED GENES; HUMAN GENOME; RECONSTRUCTION; EVOLUTION; HISTORY;

D O I：

暂无

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 axe 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.

引用

页码：126 / +

页数：2

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