Identifying similarities at metabolic pathways with a strategy of Enzymatic Step Sequences
An easy and fast strategy to compare functionally the metabolic maps is described. The KEGG metabolic maps are transformed into linear Enzymatic Step Sequences (ESS) using the Breadth First Search (BFS) algorithm. To do this, the KGML files are retrieved, and directed graph representations are creat...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | MethodsX |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S221501612300119X |
| _version_ | 1797796493813350400 |
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| author | Augusto Cesar Poot-Hernandez Katya Rodriguez-Vazquez Ernesto Perez-Rueda |
| author_facet | Augusto Cesar Poot-Hernandez Katya Rodriguez-Vazquez Ernesto Perez-Rueda |
| author_sort | Augusto Cesar Poot-Hernandez |
| collection | DOAJ |
| description | An easy and fast strategy to compare functionally the metabolic maps is described. The KEGG metabolic maps are transformed into linear Enzymatic Step Sequences (ESS) using the Breadth First Search (BFS) algorithm. To do this, the KGML files are retrieved, and directed graph representations are created; where the nodes represent enzymes or enzymatic complexes, and the edges represent a compound, that is the 'product' from one reaction and a 'substrate' for the next. Then, a set of initialization nodes are selected, and used as the root for the construction of the BFS tree. This tree is used as a guide to the construction of the ESS. From each leaf (terminal node), the path is traced backwards until it reaches the root metabolic map and with two or fewer neighbors in the graph. In a second step, the ESS are compared with a Dynamic Programing algorithm, considering an “ad hoc” substitution matrix, and minimizing the global score. The dissimilarity values between two EC numbers ranged from 0 to 1, where 0 indicates similar EC numbers, and 1 indicates different EC numbers. Finally, the alignment is evaluated by using the normalized entropy-based function, considering a threshold of ≤ 0.27 as significant. • The KEGG metabolic maps are transformed into linear Enzymatic Step Sequences (ESS) using the Breadth First Search (BFS) algorithm. • Nodes represent enzymes or enzymatic complexes, and the edges represent a compound, that is 'product' from one reaction and a 'substrate' for the next. • The ESS are compared with a Dynamic Programing algorithm, considering an “ad hoc” substitution matrix, and minimizing the global score. |
| first_indexed | 2024-03-13T03:33:55Z |
| format | Article |
| id | doaj.art-f039a192681c48beb03c802594e40a82 |
| institution | Directory Open Access Journal |
| issn | 2215-0161 |
| language | English |
| last_indexed | 2024-03-13T03:33:55Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | MethodsX |
| spelling | doaj.art-f039a192681c48beb03c802594e40a822023-06-24T05:17:24ZengElsevierMethodsX2215-01612023-01-0110102118Identifying similarities at metabolic pathways with a strategy of Enzymatic Step SequencesAugusto Cesar Poot-Hernandez0Katya Rodriguez-Vazquez1Ernesto Perez-Rueda2Unidad de Bioinformática y Manejo de la Información. Instituto de Fisiología Celular. Universidad Nacional Autónoma de México, Ciudad Universitaria, México, MexicoDepartamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, MexicoInstituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán. Mérida, Yucatán. Mexico; Corresponding author.An easy and fast strategy to compare functionally the metabolic maps is described. The KEGG metabolic maps are transformed into linear Enzymatic Step Sequences (ESS) using the Breadth First Search (BFS) algorithm. To do this, the KGML files are retrieved, and directed graph representations are created; where the nodes represent enzymes or enzymatic complexes, and the edges represent a compound, that is the 'product' from one reaction and a 'substrate' for the next. Then, a set of initialization nodes are selected, and used as the root for the construction of the BFS tree. This tree is used as a guide to the construction of the ESS. From each leaf (terminal node), the path is traced backwards until it reaches the root metabolic map and with two or fewer neighbors in the graph. In a second step, the ESS are compared with a Dynamic Programing algorithm, considering an “ad hoc” substitution matrix, and minimizing the global score. The dissimilarity values between two EC numbers ranged from 0 to 1, where 0 indicates similar EC numbers, and 1 indicates different EC numbers. Finally, the alignment is evaluated by using the normalized entropy-based function, considering a threshold of ≤ 0.27 as significant. • The KEGG metabolic maps are transformed into linear Enzymatic Step Sequences (ESS) using the Breadth First Search (BFS) algorithm. • Nodes represent enzymes or enzymatic complexes, and the edges represent a compound, that is 'product' from one reaction and a 'substrate' for the next. • The ESS are compared with a Dynamic Programing algorithm, considering an “ad hoc” substitution matrix, and minimizing the global score.http://www.sciencedirect.com/science/article/pii/S221501612300119XEnzyme commission numberMetabolic pathwaysEnzymatic step sequencesKEGGComparative genomics |
| spellingShingle | Augusto Cesar Poot-Hernandez Katya Rodriguez-Vazquez Ernesto Perez-Rueda Identifying similarities at metabolic pathways with a strategy of Enzymatic Step Sequences MethodsX Enzyme commission number Metabolic pathways Enzymatic step sequences KEGG Comparative genomics |
| title | Identifying similarities at metabolic pathways with a strategy of Enzymatic Step Sequences |
| title_full | Identifying similarities at metabolic pathways with a strategy of Enzymatic Step Sequences |
| title_fullStr | Identifying similarities at metabolic pathways with a strategy of Enzymatic Step Sequences |
| title_full_unstemmed | Identifying similarities at metabolic pathways with a strategy of Enzymatic Step Sequences |
| title_short | Identifying similarities at metabolic pathways with a strategy of Enzymatic Step Sequences |
| title_sort | identifying similarities at metabolic pathways with a strategy of enzymatic step sequences |
| topic | Enzyme commission number Metabolic pathways Enzymatic step sequences KEGG Comparative genomics |
| url | http://www.sciencedirect.com/science/article/pii/S221501612300119X |
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