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TCBB
2011
15 years 1 months ago
Graph Comparison by Log-Odds Score Matrices with Application to Protein Topology Analysis
A TOPS diagram is a simplified description of the topology of a protein using a graph where nodes are α-helices and β-strands, and edges correspond to chirality relations and p...
J. Rocha
IPL
2010
71views more  IPL 2010»
15 years 4 months ago
New common ancestor problems in trees and directed acyclic graphs
We derive a new generalization of lowest common ancestors (LCAs) in dags, called the lowest single common ancestor (LSCA). We show how to preprocess a static dag in linear time su...
Johannes Fischer, Daniel H. Huson
CPM
2004
Springer
156views Combinatorics» more  CPM 2004»
15 years 11 months ago
A Computational Model for RNA Multiple Structural Alignment.
Abstract. This paper addresses the problem of aligning multiple sequences of non-coding RNA genes. We approach this problem with the biologically motivated paradigm that scoring of...
Eugene Davydov, Serafim Batzoglou
TCBB
2011
15 years 1 months ago
Comparison of Galled Trees
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and ...
Gabriel Cardona, Mercè Llabrés, Fran...
COCOON
2003
Springer
15 years 11 months ago
On a Conjecture on Wiener Indices in Combinatorial Chemistry
Drugs and other chemical compounds are often modeled as polygonal shapes, where each vertex represents an atom of the molecule, and covalent bonds between atoms are represented by...
Yih-En Andrew Ban, Sergei Bespamyatnikh, Nabil H. ...