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A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment.

Taeho Kim¹, Hyun Joo

¹Department of Physiology and Integrated Biosystems, College of Medicine, Inje University, Busan 614-735, South Korea.

BMC Bioinformatics

|September 21, 2010

Summary

This summary is machine-generated.

ClustalXeed is a new software for multiple sequence alignment that efficiently handles large biological datasets by using both RAM and distributed storage. It overcomes memory limitations, enabling faster and easier alignment of extensive DNA and protein sequence sets.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Increasing demand for large-scale biological sequence data alignment.
Limitations of existing multiple sequence alignment (MSA) programs in handling large datasets due to HPC and storage constraints.

Purpose of the Study:

To develop a scalable software system for multiple sequence alignment capable of processing large biological sequence datasets.
To improve upon existing ClustalX and ClustalW-MPI software for enhanced performance and capacity.

Main Methods:

Designed ClustalXeed, a novel software system for multiple sequence alignment.
Utilized both physical random access memory (RAM) and a distributed file-allocation system to overcome memory dependency.
Implemented an efficient load-balancing algorithm, 'idle node-seeking task algorithm' (INSTA), to improve disk-storage system efficiency.
Integrated a graphical user interface (GUI) for user-friendly access to parallel computing.

Main Results:

ClustalXeed demonstrates the ability to align large families of protein or nucleic acid sequences.
Successfully addressed conventional memory-dependency issues in sequence alignment.
Markedly improved computation efficiency of disk-storage systems through INSTA.
Enabled fast and easy alignment of large DNA and protein sequence sets.

Conclusions:

ClustalXeed can compute large biological sequence datasets previously intractable for other MSA programs.
Enhanced storage-handling capabilities allow tackling larger sequence alignment problems.
INSTA algorithm improves processing times, especially for sequences of non-uniform length.
Supports both single PC and distributed cluster systems for flexible deployment.