Reconstruction of phyletic trees by global alignment of multiple metabolic networks
Background: In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic...
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Biomed Central Ltd.
2013
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| Online Access: | http://hdl.handle.net/1721.1/78648 https://orcid.org/0000-0002-2724-7228 |
| _version_ | 1826208811858264064 |
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| author | Ma, Cheng-Yu Lin, Shu-Hsi Lee, Chi-Ching Tang, Chuan Yi Berger, Bonnie Liao, Chung-Shou |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Ma, Cheng-Yu Lin, Shu-Hsi Lee, Chi-Ching Tang, Chuan Yi Berger, Bonnie Liao, Chung-Shou |
| author_sort | Ma, Cheng-Yu |
| collection | MIT |
| description | Background: In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. In contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information.
Results: We explored the phylogenetic relationships between microorganisms through global alignment of multiple metabolic networks. The proposed approach integrates sequence homology data with topological information of metabolic networks. In general, compared to recent studies, the resulting trees reflect the living style of organisms as well as classical taxa. Moreover, for phylogenetically closely related organisms, the classification results are consistent with specific metabolic characteristics, such as the light-harvesting systems, fermentation types, and sources of electrons in photosynthesis.
Conclusions: We demonstrate the usefulness of global alignment of multiple metabolic networks to infer phylogenetic relationships between species. In addition, our exhaustive analysis of microbial metabolic pathways reveals differences in metabolic features between phylogenetically closely related organisms. With the ongoing increase in the number of genomic sequences and metabolic annotations, the proposed approach will help identify phenotypic variations that may not be apparent based solely on sequence-based classification. |
| first_indexed | 2024-09-23T14:12:42Z |
| format | Article |
| id | mit-1721.1/78648 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:12:42Z |
| publishDate | 2013 |
| publisher | Biomed Central Ltd. |
| record_format | dspace |
| spelling | mit-1721.1/786482022-10-01T19:47:15Z Reconstruction of phyletic trees by global alignment of multiple metabolic networks Ma, Cheng-Yu Lin, Shu-Hsi Lee, Chi-Ching Tang, Chuan Yi Berger, Bonnie Liao, Chung-Shou Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Mathematics Berger, Bonnie Background: In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. In contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information. Results: We explored the phylogenetic relationships between microorganisms through global alignment of multiple metabolic networks. The proposed approach integrates sequence homology data with topological information of metabolic networks. In general, compared to recent studies, the resulting trees reflect the living style of organisms as well as classical taxa. Moreover, for phylogenetically closely related organisms, the classification results are consistent with specific metabolic characteristics, such as the light-harvesting systems, fermentation types, and sources of electrons in photosynthesis. Conclusions: We demonstrate the usefulness of global alignment of multiple metabolic networks to infer phylogenetic relationships between species. In addition, our exhaustive analysis of microbial metabolic pathways reveals differences in metabolic features between phylogenetically closely related organisms. With the ongoing increase in the number of genomic sequences and metabolic annotations, the proposed approach will help identify phenotypic variations that may not be apparent based solely on sequence-based classification. National Institutes of Health (U.S.) (Grant GM081871) 2013-05-01T15:47:55Z 2013-05-01T15:47:55Z 2013-01 Article http://purl.org/eprint/type/JournalArticle 1471-2105 http://hdl.handle.net/1721.1/78648 Ma, Cheng-Yu et al. “Reconstruction of phyletic trees by global alignment of multiple metabolic networks.” BMC Bioinformatics 14.2 (2013). https://orcid.org/0000-0002-2724-7228 en_US http://www.biomedcentral.com/1471-2105/14/S2/S12/abstract BMC Bioinformatics Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 application/pdf Biomed Central Ltd. BioMed Central |
| spellingShingle | Ma, Cheng-Yu Lin, Shu-Hsi Lee, Chi-Ching Tang, Chuan Yi Berger, Bonnie Liao, Chung-Shou Reconstruction of phyletic trees by global alignment of multiple metabolic networks |
| title | Reconstruction of phyletic trees by global alignment of multiple metabolic networks |
| title_full | Reconstruction of phyletic trees by global alignment of multiple metabolic networks |
| title_fullStr | Reconstruction of phyletic trees by global alignment of multiple metabolic networks |
| title_full_unstemmed | Reconstruction of phyletic trees by global alignment of multiple metabolic networks |
| title_short | Reconstruction of phyletic trees by global alignment of multiple metabolic networks |
| title_sort | reconstruction of phyletic trees by global alignment of multiple metabolic networks |
| url | http://hdl.handle.net/1721.1/78648 https://orcid.org/0000-0002-2724-7228 |
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