Fast and Accurate Multiple Sequence Alignment with MSAProbs-MPI

González-Domínguez, Jorge

doi:10.1007/978-1-0716-1036-7_3

Cited by 3 publications

(1 citation statement)

References 24 publications

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“…The synchronization of PSAs with the proposed decision diagram effectively incorporates modeling the MSA problem within polynomial space complexity. Moreover, Domínguez [53] delves into statistical and biological concepts employed in the MSAProbs-MPI tool to complete the alignments where high-performance computing techniques are employed for alignment acceleration. Additionally, Ju et al [54] introduced an end-to-end deep neural network and called it CopulaNe, designed to directly estimate residue co-evolution from MSA, representing a cutting-edge approach in the finding of exact solutions for MSA.…”

Section: Multiple Sequence Alignmentmentioning

confidence: 99%

Accelerating Multiple Sequence Alignments Using Parallel Computing

Bani Baker,

Al-Hussien,

Al-Ayyoub

2024

Computation

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Multiple sequence alignment (MSA) stands as a critical tool for understanding the evolutionary and functional relationships among biological sequences. Obtaining an exact solution for MSA, termed exact-MSA, is a significant challenge due to the combinatorial nature of the problem. Using the dynamic programming technique to solve MSA is recognized as a highly computationally complex algorithm. To cope with the computational demands of MSA, parallel computing offers the potential for significant speedup in MSA. In this study, we investigated the utilization of parallelization to solve the exact-MSA using three proposed novel approaches. In these approaches, we used multi-threading techniques to improve the performance of the dynamic programming algorithms in solving the exact-MSA. We developed and employed three parallel approaches, named diagonal traversing, blocking, and slicing, to improve MSA performance. The proposed method accelerated the exact-MSA algorithm by around 4×. The suggested approaches could be basic approaches to be combined with many existing techniques. These proposed approaches could serve as foundational elements, offering potential integration with existing techniques for comprehensive MSA enhancement.

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Section: Multiple Sequence Alignmentmentioning

confidence: 99%

Accelerating Multiple Sequence Alignments Using Parallel Computing

Bani Baker,

Al-Hussien,

Al-Ayyoub

2024

Computation

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Multiple Sequence Alignment

Sayood

Otu

2022

Synthesis Lectures on Biomedical Engineering

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A survey on the algorithm and development of multiple sequence alignment

Yong-qing

Qiang

Zhou

et al. 2022

Briefings in Bioinformatics

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Multiple sequence alignment (MSA) is an essential cornerstone in bioinformatics, which can reveal the potential information in biological sequences, such as function, evolution and structure. MSA is widely used in many bioinformatics scenarios, such as phylogenetic analysis, protein analysis and genomic analysis. However, MSA faces new challenges with the gradual increase in sequence scale and the increasing demand for alignment accuracy. Therefore, developing an efficient and accurate strategy for MSA has become one of the research hotspots in bioinformatics. In this work, we mainly summarize the algorithms for MSA and its applications in bioinformatics. To provide a structured and clear perspective, we systematically introduce MSA’s knowledge, including background, database, metric and benchmark. Besides, we list the most common applications of MSA in the field of bioinformatics, including database searching, phylogenetic analysis, genomic analysis, metagenomic analysis and protein analysis. Furthermore, we categorize and analyze classical and state-of-the-art algorithms, divided into progressive alignment, iterative algorithm, heuristics, machine learning and divide-and-conquer. Moreover, we also discuss the challenges and opportunities of MSA in bioinformatics. Our work provides a comprehensive survey of MSA applications and their relevant algorithms. It could bring valuable insights for researchers to contribute their knowledge to MSA and relevant studies.

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Fast and Accurate Multiple Sequence Alignment with MSAProbs-MPI

Cited by 3 publications

References 24 publications

Accelerating Multiple Sequence Alignments Using Parallel Computing

Accelerating Multiple Sequence Alignments Using Parallel Computing

Multiple Sequence Alignment

A survey on the algorithm and development of multiple sequence alignment

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