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BIOMAPP::CHIP: large-scale motif analysis.
Garbelini, Jader M Caldonazzo; Sanches, Danilo S; Pozo, Aurora T Ramirez.
Afiliación
  • Garbelini JMC; Department of Informatics, Federal University of Parana, XV de Novembro Street, Curitiba, Parana, 80060000, Brazil. jmcgarbelini@inf.ufpr.br.
  • Sanches DS; Department of Informatics, Federal University of Technology, Alberto Carazzai Avenue, Cornelio Procopio, Parana, 86300000, Brazil.
  • Pozo ATR; Department of Informatics, Federal University of Parana, XV de Novembro Street, Curitiba, Parana, 80060000, Brazil.
BMC Bioinformatics ; 25(1): 128, 2024 Mar 26.
Article en En | MEDLINE | ID: mdl-38528492
ABSTRACT

BACKGROUND:

Discovery biological motifs plays a fundamental role in understanding regulatory mechanisms. Computationally, they can be efficiently represented as kmers, making the counting of these elements a critical aspect for ensuring not only the accuracy but also the efficiency of the analytical process. This is particularly useful in scenarios involving large data volumes, such as those generated by the ChIP-seq protocol. Against this backdrop, we introduce BIOMAPPCHIP, a tool specifically designed to optimize the discovery of biological motifs in large data volumes.

RESULTS:

We conducted a comprehensive set of comparative tests with state-of-the-art algorithms. Our analyses revealed that BIOMAPPCHIP outperforms existing approaches in various metrics, excelling both in terms of performance and accuracy. The tests demonstrated a higher detection rate of significant motifs and also greater agility in the execution of the algorithm. Furthermore, the SMT component played a vital role in the system's efficiency, proving to be both agile and accurate in kmer counting, which in turn improved the overall efficacy of our tool.

CONCLUSION:

BIOMAPPCHIP represent real advancements in the discovery of biological motifs, particularly in large data volume scenarios, offering a relevant alternative for the analysis of ChIP-seq data and have the potential to boost future research in the field. This software can be found at the following address (https//github.com/jadermcg/biomapp-chip).
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Algoritmos / Programas Informáticos Idioma: En Revista: BMC Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2024 Tipo del documento: Article País de afiliación: Brasil Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Algoritmos / Programas Informáticos Idioma: En Revista: BMC Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2024 Tipo del documento: Article País de afiliación: Brasil Pais de publicación: Reino Unido