An approach for determining evolutionary distance in network-based phylogenetic analysis

  • Authors:

  • Tingting Zhou;Keith C. C. Chan;Yi Pan;Zhenghua Wang

  • Affiliations:

  • National Laboratory for Paralleling and Distributed Processing, School of Computer, National University of Defense Technology, Changsha, Hunan, P.R. of China and Department of computing, The Hong ...;Department of computing, The Hong Kong Polytechnic University, Hong Kong, China;Department of Computer Science, Georgia State University, Atlanta, GA;National Laboratory for Paralleling and Distributed Processing, School of Computer, National University of Defense Technology, Changsha, Hunan, P.R. of China

  • Venue:
  • ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
  • Year:
  • 2008

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Abstract

Network-based phylogenetic analysis explores phylogenetic relationshipsamong different organisms by comparing their biological networks, especiallymetabolic networks. The differences between networks, often expressedas evolutionary distances, are normally measured using the plain Jaccard distance.In this paper, we show enzymes are different in phylogenetic conservationand topological importance, which are correlated significantly. Inspired bythis observation, we propose a new approach to determine evolutionary distances.Our approach considers not only the number of different enzymes indifferent organisms, but also the phylogenetic or topological difference of individualenzymes. The resulting evolutionary distance measures are comparedwith the plain Jaccard distance by use of 16s rRNA-based distance as reference.It shows that new distance measures make errors smaller in all test casesof comparison.