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SaAlign: Multiple DNA/RNA sequence alignment and phylogenetic tree construction tool for ultra-large datasets and
Ziyuan Wang1, Junjie Tan2, Yanling Long3
1Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, PR China.
Computational and Structural Biotechnology Journal
|April 15, 2022
Summary
A new tool, SaAlign, optimizes DNA/RNA sequence alignment for large datasets and long sequences, improving computational efficiency. It outperforms existing tools like MAFFT for ultra-large mitochondrial genome analysis.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Multiple DNA/RNA sequence alignment is crucial for bioinformatics, particularly phylogenetic tree construction.
- Increasing DNA sequencing data necessitates optimized bioinformatics tools for handling large and long sequences.
- Mitochondochondrial genome analysis requires efficient software, but existing tools struggle with ultra-large datasets.
Purpose of the Study:
- To develop and optimize a novel tool for efficient multiple DNA/RNA sequence alignment, especially for ultra-large datasets and long sequences.
- To improve computational space and time efficiency in sequence alignment.
- To provide a significant resource for whole-genome and whole-mitochondrial genome research, particularly in plants.
Main Methods:
- Optimization of a dynamic programming algorithm using longest common substring methods.
- Implementation of a multiple DNA/RNA sequence alignment tool utilizing Center Star strategy and suffix array algorithm.
- Testing with ultra-large DNA datasets, including sequences over 300 kb, and mitochondrial genome datasets.
Main Results:
- The developed tool, SaAlign (Multiple DNA/RNA Sequence Alignment Tool Based on Suffix Tree), demonstrated significant savings in time and computational space.
- SaAlign outperformed existing tools such as MAFFT and HAlign-II in aligning ultra-large datasets.
- MAFFT encountered core dump errors with ultra-large mitochondrial genome datasets, highlighting SaAlign's superior capability.
Conclusions:
- SaAlign offers a highly efficient solution for multiple DNA/RNA sequence alignment, particularly for large-scale genomic studies.
- The tool's optimization of computational resources is significant for laboratories utilizing whole-genome research and Next-Generation Sequencing (NGS) technologies.
- SaAlign is especially valuable for plant whole-mitochondrial genome research, addressing current limitations in sequence alignment software.
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