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

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Scopus citations

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.

Original language	English
Title of host publication	Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	109-113
Number of pages	5
ISBN (Electronic)	9781728116914
DOIs	https://doi.org/10.1109/IESTEC46403.2019.00028
State	Published - Oct 2019
Event	7th International Engineering, Sciences and Technology Conference, IESTEC 2019 - Panama City, Panama Duration: 9 Oct 2019 → 11 Oct 2019

Publication series

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

Conference

Conference	7th International Engineering, Sciences and Technology Conference, IESTEC 2019
Country/Territory	Panama
City	Panama City
Period	9/10/19 → 11/10/19

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 7 Affordable and Clean Energy

Keywords

Breadth-first traversal
Depth-first traversal
Metabolic pathways
Sequence alignments

Access to Document

10.1109/IESTEC46403.2019.00028

Cite this

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. In Proceedings - 2019 7th International Engineering, Sciences and Technology Conference, IESTEC 2019 (pp. 109-113). Article 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",

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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. in 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, Panama, 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).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Stalley, Seth

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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. In 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

Abstract

Publication series

Conference

UN SDGs

Keywords

Access to Document

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