G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era

Johan S. Piña; Simon Orozco-Arias; Nicolas Tobón-Orozco; Leonardo Camargo-Forero; Reinel Tabares-Soto; Romain Guyot

doi:10.1177/11769343221150585

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G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era

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G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era

Johan S. Piña, Simon Orozco-Arias, Nicolas Tobón-Orozco, Leonardo Camargo-Forero, Reinel Tabares-Soto et Romain Guyot

Evolutionary bioinformatics online, Vol.19, p.11769343221150585

01/01/2023

DOI: https://doi.org/10.1177/11769343221150585

PMID: 36703866

Résumé

Original Research

A common task in bioinformatics is to compare DNA sequences to identify similarities between organisms at the sequence level. An approach to such comparison is the dot-plots, a 2-dimensional graphical representation to analyze DNA or protein alignments. Dot-plots alignment software existed before the sequencing revolution, and now there is an ongoing limitation when dealing with large-size sequences, resulting in very long execution times. High-Performance Computing (HPC) techniques have been successfully used in many applications to reduce computing times, but so far, very few applications for graphical sequence alignment using HPC have been reported. Here, we present G-SAIP (Graphical Sequence Alignment in Parallel), a software capable of spawning multiple distributed processes on CPUs, over a supercomputing infrastructure to speed up the execution time for dot-plot generation up to 1.68× compared with other current fastest tools, improve the efficiency for comparative structural genomic analysis, phylogenetics because the benefits of pairwise alignments for comparison between genomes, repetitive structure identification, and assembly quality checking.

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Titre: G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era
Créateurs - sans rôle: Johan S. Piña - Department of Data Science, People Contact, Manizales, Caldas, Colombia Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia UbiHPC, Bucaramanga, Colombia Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Institut de Recherche pour le Développement, CIRAD, University of Montpellier, Montpellier, France
Simon Orozco-Arias - Department of Data Science, People Contact, Manizales, Caldas, Colombia Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia UbiHPC, Bucaramanga, Colombia Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Institut de Recherche pour le Développement, CIRAD, University of Montpellier, Montpellier, France
Nicolas Tobón-Orozco - Department of Data Science, People Contact, Manizales, Caldas, Colombia Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia UbiHPC, Bucaramanga, Colombia Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Institut de Recherche pour le Développement, CIRAD, University of Montpellier, Montpellier, France
Leonardo Camargo-Forero - Department of Data Science, People Contact, Manizales, Caldas, Colombia Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia UbiHPC, Bucaramanga, Colombia Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Institut de Recherche pour le Développement, CIRAD, University of Montpellier, Montpellier, France
Reinel Tabares-Soto - Department of Data Science, People Contact, Manizales, Caldas, Colombia Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia UbiHPC, Bucaramanga, Colombia Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Institut de Recherche pour le Développement, CIRAD, University of Montpellier, Montpellier, France
Romain Guyot - Department of Data Science, People Contact, Manizales, Caldas, Colombia Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia UbiHPC, Bucaramanga, Colombia Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia Institut de Recherche pour le Développement, CIRAD, University of Montpellier, Montpellier, France
Détails de publication: Evolutionary bioinformatics online, Vol.19, p.11769343221150585
Éditeur: SAGE Publications
Note de subvention: 785/2017 / ; 752-115 / ; 0319120 / ;
Identifiants: 99136548609311
Unité académique: Diversité, Adaptation et Développement des plantes - DIADE
Langue: English
Type de ressource: Journal article