A web tool for executing low cost algorithms for metabolic pathway comparison based on graph similarity

Esteban Arias-Mendez; Kevin Castro-Fuentes; Seth Stalley; Pablo Vargas-Rosales

doi:10.1109/IESTEC46403.2019.00028

A web tool for executing low cost algorithms for metabolic pathway comparison based on graph similarity

Esteban Arias-Mendez
, Kevin Castro-Fuentes
, Seth Stalley
, Pablo Vargas-Rosales

Costa Rica Institute of Technology

Producción científica: Capítulo del libro/informe/acta de congreso › Contribución a la conferencia › revisión exhaustiva

1 Cita (Scopus)

Resumen

Metabolic pathways contain a huge amount of information ready to be exploited. Metabolic Pathway comparison can help to evaluate evolutionary aspects, industrially important routes, or novel medicines. Pathway or graph comparison has been described to be NP. Here we present a web tool that runs low-cost algorithms proposed for pathway comparison between graphs representing metabolic pathways. The first algorithm converts the graph into a 1D structure and then generates alignment scores; while the second one details the similarities and differences between the input pathways. The tool proved to be a good source of criteria for the evaluation of metabolic pathways comparison. The simplification of the methods does not affect the significance of the similarity obtained. The tool can be accessed through the URL: ebro.ec.tec.ac.cr.

Idioma original	Inglés
Título de la publicación alojada	Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019
Editorial	Institute of Electrical and Electronics Engineers Inc.
Páginas	109-113
Número de páginas	5
ISBN (versión digital)	9781728116914
DOI	https://doi.org/10.1109/IESTEC46403.2019.00028
Estado	Publicada - oct 2019
Evento	7th International Engineering, Sciences and Technology Conference, IESTEC 2019 - Panama City, Panamá Duración: 9 oct 2019 → 11 oct 2019

Serie de la publicación

Nombre	Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019

Conferencia

Conferencia	7th International Engineering, Sciences and Technology Conference, IESTEC 2019
País/Territorio	Panamá
Ciudad	Panama City
Período	9/10/19 → 11/10/19

ODS de las Naciones Unidas

Este resultado contribuye a los siguientes Objetivos de Desarrollo Sostenible

ODS 7: Energía asequible y no contaminante

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10.1109/IESTEC46403.2019.00028

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Arias-Mendez, E., Castro-Fuentes, K., Stalley, S., & Vargas-Rosales, P. (2019). A web tool for executing low cost algorithms for metabolic pathway comparison based on graph similarity. En Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019 (pp. 109-113). Artículo 8943599 (Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/IESTEC46403.2019.00028

Arias-Mendez, Esteban ; Castro-Fuentes, Kevin ; Stalley, Seth et al. / A web tool for executing low cost algorithms for metabolic pathway comparison based on graph similarity. Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019. Institute of Electrical and Electronics Engineers Inc., 2019. pp. 109-113 (Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019).

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abstract = "Metabolic pathways contain a huge amount of information ready to be exploited. Metabolic Pathway comparison can help to evaluate evolutionary aspects, industrially important routes, or novel medicines. Pathway or graph comparison has been described to be NP. Here we present a web tool that runs low-cost algorithms proposed for pathway comparison between graphs representing metabolic pathways. The first algorithm converts the graph into a 1D structure and then generates alignment scores; while the second one details the similarities and differences between the input pathways. The tool proved to be a good source of criteria for the evaluation of metabolic pathways comparison. The simplification of the methods does not affect the significance of the similarity obtained. The tool can be accessed through the URL: ebro.ec.tec.ac.cr.",

keywords = "Breadth-first traversal, Depth-first traversal, Metabolic pathways, Sequence alignments",

author = "Esteban Arias-Mendez and Kevin Castro-Fuentes and Seth Stalley and Pablo Vargas-Rosales",

note = "Publisher Copyright: {\textcopyright} 2019 IEEE.; 7th International Engineering, Sciences and Technology Conference, IESTEC 2019 ; Conference date: 09-10-2019 Through 11-10-2019",

year = "2019",

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Arias-Mendez, E, Castro-Fuentes, K, Stalley, S & Vargas-Rosales, P 2019, A web tool for executing low cost algorithms for metabolic pathway comparison based on graph similarity. En Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019., 8943599, Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019, Institute of Electrical and Electronics Engineers Inc., pp. 109-113, 7th International Engineering, Sciences and Technology Conference, IESTEC 2019, Panama City, Panamá, 9/10/19. https://doi.org/10.1109/IESTEC46403.2019.00028

A web tool for executing low cost algorithms for metabolic pathway comparison based on graph similarity. / Arias-Mendez, Esteban; Castro-Fuentes, Kevin; Stalley, Seth et al.
Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019. Institute of Electrical and Electronics Engineers Inc., 2019. p. 109-113 8943599 (Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019).

Producción científica: Capítulo del libro/informe/acta de congreso › Contribución a la conferencia › revisión exhaustiva

TY - GEN

T1 - A web tool for executing low cost algorithms for metabolic pathway comparison based on graph similarity

AU - Arias-Mendez, Esteban

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AU - Stalley, Seth

AU - Vargas-Rosales, Pablo

PY - 2019/10

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N2 - Metabolic pathways contain a huge amount of information ready to be exploited. Metabolic Pathway comparison can help to evaluate evolutionary aspects, industrially important routes, or novel medicines. Pathway or graph comparison has been described to be NP. Here we present a web tool that runs low-cost algorithms proposed for pathway comparison between graphs representing metabolic pathways. The first algorithm converts the graph into a 1D structure and then generates alignment scores; while the second one details the similarities and differences between the input pathways. The tool proved to be a good source of criteria for the evaluation of metabolic pathways comparison. The simplification of the methods does not affect the significance of the similarity obtained. The tool can be accessed through the URL: ebro.ec.tec.ac.cr.

AB - Metabolic pathways contain a huge amount of information ready to be exploited. Metabolic Pathway comparison can help to evaluate evolutionary aspects, industrially important routes, or novel medicines. Pathway or graph comparison has been described to be NP. Here we present a web tool that runs low-cost algorithms proposed for pathway comparison between graphs representing metabolic pathways. The first algorithm converts the graph into a 1D structure and then generates alignment scores; while the second one details the similarities and differences between the input pathways. The tool proved to be a good source of criteria for the evaluation of metabolic pathways comparison. The simplification of the methods does not affect the significance of the similarity obtained. The tool can be accessed through the URL: ebro.ec.tec.ac.cr.

KW - Breadth-first traversal

KW - Depth-first traversal

KW - Metabolic pathways

KW - Sequence alignments

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Arias-Mendez E, Castro-Fuentes K, Stalley S, Vargas-Rosales P. A web tool for executing low cost algorithms for metabolic pathway comparison based on graph similarity. En Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019. Institute of Electrical and Electronics Engineers Inc. 2019. p. 109-113. 8943599. (Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019). doi: 10.1109/IESTEC46403.2019.00028

A web tool for executing low cost algorithms for metabolic pathway comparison based on graph similarity

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