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bioRxiv · 10.1101/2023.11.06.565033

biomapp::chip: Large-Scale Motif Analysis

Caldonazzo Garbelini, J. M.·Sanches, D. S.·Ramirez Pozo, A. T.
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Abstract

BackgroundDiscovery 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 O_SCPLOWBIOMAPPC_SCPLOWO_SCPCAP ::C_SCPCAPO_SCPLOWCHIPC_SCPLOW, a tool specifically designed to optimize the discovery of biological motifs in large data volumes. ResultsWe conducted a comprehensive set of comparative tests with state-of-the-art algorithms. Our analyses revealed that O_SCPLOWBIOMAPPC_SCPLOWO_SCPCAP ::C_SCPCAPO_SCPLOWCHIPC_SCPLOW 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 O_SCPLOWSMTC_SCPLOW component played a vital role in the systems efficiency, proving to be both agile and accurate in kmer counting, which in turn improved the overall efficacy of our tool. ConclusionO_SCPLOWBIOMAPPC_SCPLOWO_SCPCAP ::C_SCPCAPO_SCPLOWCHIPC_SCPLOW 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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Caldonazzo Garbelini, J. M., Sanches, D. S., Ramirez Pozo, A. T.. 2023-11-07. biomapp::chip: Large-Scale Motif Analysis. https://doi.org/10.1101/2023.11.06.565033

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