Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Low-Cost Algorithms for Metabolic Pathway Pairwise Comparison

Version 1 : Received: 13 May 2021 / Approved: 18 May 2021 / Online: 18 May 2021 (10:45:18 CEST)

How to cite: Arias-Méndez, E.; Barquero-Morera, D.; Torres-Rojas, F.J. Low-Cost Algorithms for Metabolic Pathway Pairwise Comparison. Preprints 2021, 2021050415 (doi: 10.20944/preprints202105.0415.v1). Arias-Méndez, E.; Barquero-Morera, D.; Torres-Rojas, F.J. Low-Cost Algorithms for Metabolic Pathway Pairwise Comparison. Preprints 2021, 2021050415 (doi: 10.20944/preprints202105.0415.v1).

Abstract

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.

Subject Areas

metabolic pathways; graph comparison; graph alignment; graph depth-first traversal; graph breadth-first traversal; global alignment; local alignment; semiglobal alignment

Comments (0)

We encourage comments and feedback from a broad range of readers. See criteria for comments and our diversity statement.

Leave a public comment
Send a private comment to the author(s)
Views 0
Downloads 0
Comments 0
Metrics 0


×
Alerts
Notify me about updates to this article or when a peer-reviewed version is published.
We use cookies on our website to ensure you get the best experience.
Read more about our cookies here.