Algorithms of ancestral gene length reconstruction

Biomed Res Int. 2013:2013:472163. doi: 10.1155/2013/472163. Epub 2013 Nov 26.

Abstract

Ancestral sequence reconstruction is a well-known problem in molecular evolution. The problem presented in this study is inspired by sequence reconstruction, but instead of leaf-associated sequences we consider only their lengths. We call this problem ancestral gene length reconstruction. It is a problem of finding an optimal labeling which minimizes the total length's sum of the edges, where both a tree and nonnegative integers associated with corresponding leaves of the tree are the input. In this paper we give a linear algorithm to solve the problem on binary trees for the Manhattan cost function s(v, w) = |π(v) - π(w)|.

MeSH terms

  • Algorithms
  • Conserved Sequence / genetics*
  • Evolution, Molecular*
  • Models, Theoretical*
  • Sequence Analysis, DNA