Alternative low cost algorithms for metabolic pathway comparison

Arias-Méndez, Esteban; Torres-Rojas, Francisco J.

doi:10.1109/iwobi.2017.7985545

Cited by 5 publications

(8 citation statements)

References 14 publications

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“…In a previous work [3], two different low-cost algorithms were developed as simple mechanisms for the comparison of two metabolic pathways that can be used as a previous step to a deeper and more time-consuming analysis to be applied for the graph comparison associated to the pathways.…”

Section: Metabolic Pathways and Graphsmentioning

confidence: 99%

“…The results are correlated later to the numerical values of the first proposal to validate the differences found. The process is thoroughly explained in [3]. However on figure 9 a summary of the process is shown.…”

Section: Algorithm 2: Differentiation By Pairsmentioning

confidence: 99%

“…The database also categorizes metabolic pathways according to their biological functions and classes of metabolites involved in the reactions. It does so with a hierarchy of pathway classes, where each class composes a large group of sub-classes and pathways, first grouping them by general characteristics (for example, "Biosynthesis"), and further down the hierarchy, forming detailed classes containing only pathways (for example, "Glycogen and Starch Biosynthesis") 3 . In this work, we refer to those categories as "families" of metabolic pathways.…”

Section: Algorithm 2: Differentiation By Pairsmentioning

confidence: 99%

“…Metabolic pathway comparison has been defined as a computationally complex task [1,2]. In a previous work [3], two different approaches that simplify the problem of comparing pathways represented as graphs were introduced. The first algorithm consists of the transformation of a two-dimensional graph structure, representing a metabolic pathway, to a one-dimensional structure and thus aligning the corresponding data using a reduced 1 dimension string.…”

mentioning

confidence: 99%

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Low-Cost Algorithms for Metabolic Pathway Pairwise Comparison

Arias-Méndez¹,

Barquero-Morera²,

Torres-Rojas³

2021

Preprint

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Metabolic pathways provide key information to achieve a better understanding of life and all its processes; this is useful information for the improvement of medicine, agronomy, pharmacy, and other similar areas. The main analysis tool used to study these pathways is based on the idea of pathway comparison, using graph data structures. Metabolic pathway comparison has been defined as a computationally complex task \cite{ay2011submap,abaka2013campways}. In previous work from 2017, two different approaches that simplify the problem of comparing pathways represented as graphs were introduced. The first algorithm consists of the transformation of a two-dimensional graph structure, representing a metabolic pathway, to a one-dimensional structure and thus aligning the corresponding data using a reduced 1 dimension string. The second algorithm consists of performing a paired analysis between reactions in pathways and thus eliminating all similarities, finally, showing these differences to the user. The suggestion is to use the information provided by these algorithms as a previous analysis to a deeper, more expensive, comparison tool use. Here we provide an extension of this work with more data and deeper analysis. These methods have shown to be an effective way to treat the problem of metabolic pathway comparison as listed in the discussion and results section. Our results show evidence of a quick, simple and effective way to resolve the described problem.

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Section: Metabolic Pathways and Graphsmentioning

confidence: 99%

Section: Algorithm 2: Differentiation By Pairsmentioning

confidence: 99%

Section: Algorithm 2: Differentiation By Pairsmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Low-Cost Algorithms for Metabolic Pathway Pairwise Comparison

Arias-Méndez¹,

Barquero-Morera²,

Torres-Rojas³

2021

Preprint

View full text Add to dashboard Cite

show abstract

“…On a previous work [11], two different low-cost approaches were developed as simple mechanisms for the comparison of two metabolic pathways that can be used as a previous step to a deeper and more time-consuming analysis to be applied for the graph comparison associated to the pathways. Later, as an extension of the original algorithms, they were applied to a more general kind of graphs [12].…”

Section: Algorithmsmentioning

confidence: 99%

Propuesta para la comparación de flujos metabólicos

Arias-Méndez

Montero-Marín

Torres-Rojas

2020

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El análisis de flujos metabólicos puede proporcionar información importante para una mejor comprensión de la vida y todos sus procesos, beneficiando directamente a áreas como la medicina, la agronomía, la farmacia y otras. Algunas de las principales herramientas utilizadas para estudiar y analizar las rutas metabólicas se han basado en la idea de la comparación de rutas metabólicas, utilizando estructuras de datos como grafos. Algunas de esas tareas se consideran problemas computacionales difíciles. Por otro lado, esas comparaciones aún no han tenido en cuenta el flujo metabólico como parte de la vía o proceso metabólico. Es decir, considerar cuánta cantidad de un metabolito pasa a través de un sistema de reacción con el tiempo. Proponemos aquí una forma simple de comparar rutas metabólicas utilizando su información de flujo relacionada mediante un método simple de comparación de rutas metabólicas introducido en 2017 y ajustándolo a grafos ponderados. Los algoritmos analizan los grafos ponderados asociados de las rutas de flujo metabólico y proporcionan una puntuación rápida de sus similitudes de flujo en primer lugar y una lista de similitudes y diferencias entre las rutas de flujo dadas, enumeradas como rutas. Proporcionamos algunas ideas sobre el análisis a continuación para obtener un buen sistema de puntuación al comparar grafos ponderados relacionados con las rutas metabólicas en un cálculo de bajo costo.

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