Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

PLoS One

Shinichi Shimozono¹  Hideaki Yoshida¹  Kentaro Inoue²  Hiroyuki Kurata² 

[1]Department of Artificial Intelligence, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan

[2]Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan

关键词: Algorithms;    Metabolic networks;    Xenobiotic metabolism;    Nucleotide mapping;    Optimization;    Amino acid metabolism;    Carbohydrate metabolism;    Computer software;   

DOI  :  10.1371/journal.pone.0037739

学科分类：医学（综合）

来源: Public Library of Science

【 摘 要 】

Background For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. Results We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. ConclusionsUse of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

【 授权许可】

CC BY