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HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed

Shixiang Wan1, Quan Zou1,2

  • 1School of Computer Science and Technology, Tianjin University, Tianjin, China.

Algorithms for Molecular Biology : AMB
|October 14, 2017
PubMed
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HAlign-II accelerates ultra-large multiple sequence alignment and phylogenetic tree construction using distributed computing. This efficient tool saves time and space for large biological datasets, outperforming existing software.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is vital for biological sequence analysis and phylogenetic tree construction.
  • The rapid growth of next-generation sequencing data necessitates efficient methods for handling ultra-large biological sequence files.
  • Current alignment approaches struggle with the scale and diversity of modern biological sequence data.

Purpose of the Study:

  • To develop a cost-efficient and time-efficient tool for ultra-large multiple biological sequence alignment and phylogenetic tree construction.
  • To address the limitations of existing software in handling massive biological sequence datasets.

Main Methods:

  • Implementation of HAlign-II, a tool based on the HAlign and Spark distributed computing system.
Keywords:
Distributed computingMultiple sequence alignmentPhylogenetic treesSpark

Related Experiment Videos

  • Utilizing distributed and parallel computing techniques to accelerate sequence analysis.
  • Testing HAlign-II on large-scale DNA and protein datasets exceeding 1 GB.

    • Main Results:

    • HAlign-II demonstrated significant savings in time and space for ultra-large datasets.
    • The tool outperformed existing software in efficiency and performance.
    • HAlign-II exhibits high memory efficiency and excellent scalability with increased computing resources.
    • Successful execution of MSA and phylogenetic tree construction for ultra-large sequence sets.

    Conclusions:

    • HAlign-II provides a user-friendly web server built upon a distributed computing infrastructure.
    • The open-source codes and datasets for HAlign-II are publicly available for research use.