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

Background Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different...

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Veröffentlicht in:Algorithms for molecular biology Jg. 12; H. 1; S. 25 - 10
Hauptverfasser: Wan, Shixiang, Zou, Quan
Format: Journal Article
Sprache:Englisch
Veröffentlicht: London BioMed Central 29.09.2017
BioMed Central Ltd
Springer Nature B.V
BMC
Schlagworte:
Algorithms
Alignment
Analysis
Bioinformatics
Biological analysis
Biological effects
Biomedical and Life Sciences
Cellular and Medical Topics
Computational Biology/Bioinformatics
Computer memory
Computer networks
Computing costs
Computing time
Datasets
Deoxyribonucleic acid
Design
Distributed computing
Distributed processing
DNA
DNA sequencing
Efficiency
Fault tolerance
Fourier transforms
Genomes
International conferences
Internet
Internet server software
Life Sciences
Methods
Multiple sequence alignment
Nucleotide sequence
Phylogenetic trees
Phylogenetics
Phylogeny
Physiological
Proteins
Servers
Software
Software development tools
Source code
Spark
Technology application
China
Phylogenetic trees
Spark
Multiple sequence alignment
Distributed computing
ISSN:1748-7188, 1748-7188
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Zusammenfassung:Background Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Methods Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. Results The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. Conclusions THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign .
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ISSN:1748-7188
1748-7188
DOI:10.1186/s13015-017-0116-x