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This article is part of the supplement: Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Bioinformatics

Open Access Proceedings

Reconstruction of phyletic trees by global alignment of multiple metabolic networks

Cheng-Yu Ma1, Shu-Hsi Lin2, Chi-Ching Lee13, Chuan Yi Tang14, Bonnie Berger56 and Chung-Shou Liao7*

Author Affiliations

1 Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan

2 Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan

3 Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan

4 Department of Computer Science and Information Engineering, Providence University, Taichung, Taiwan

5 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

6 Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

7 Department of Industrial Engineering and Engineering Management, National Tsing Hua University, Hsinchu, Taiwan

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BMC Bioinformatics 2013, 14(Suppl 2):S12  doi:10.1186/1471-2105-14-S2-S12

Published: 21 January 2013

Additional files

Additional file 1:

Organisms used in this study. Edges represent the reactions catalyzed by enzymes in each metabolic network. All metabolic pathways were retrieved from KEGG [19].

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Additional file 2:

Comparison of reconstructed phylogenic trees. Left: Reconstruction by Chang et al. [17]. Right: Reconstruction by Zhang et al. [12]. Reprinted under the BioMed Central Open License agreement (BMC Bioinformatics).

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Additional file 3:

The IsoRankN algorithm.

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Additional file 4:

Statistics for KEGG pathways between three pairs of organisms: (mlo, pae), (ccr, mlo) and (ccr, pae). The x axis represents KEGG pathway IDs, and the y axis represents the number of the constituent enzymes in the pathways. The two pathways ko00260 and ko00860 in the pair (mlo, pae) contain more functional orthologs than those in the pairs (ccr, mlo) and (ccr, pae).

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Additional file 5:

Statistics for KEGG pathways between two pairs of organisms in Lactobacillus: The x axis represents KEGG pathway IDs, and the y axis represents the number of the constituent enzymes in the pathways. (a) (lga, ljo) in obligate homofermentation, and (lfe, lga) from different fermentation types. (b) (lfe, lru) in obligate heterofermentation, and (lfe, lga) from different fermentation types.

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Additional file 6:

Statistics for KEGG pathways between two pairs of organisms of Prochlorococcus and Synechococcus: The x axis represents KEGG pathway IDs, and the y axis represents the number of the constituent enzymes in the pathways. (a) (pma, pmc) from Prochlorococcus, and (pma, syx) from Prochlorococcus and Synechococcus, respectively. (b) (syw, syx) from Synechococcus, and (pma, syx) from Prochlorococcus and Synechococcus, respectively.

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