ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment.
BACKGROUND
There is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited in their ability to handle very large amounts of sequences because the system lacks a scalable high-performance computing (HPC) environment with a greatly extended data storage capacity.


RESULTS
We designed ClustalXeed, a software system for multiple sequence alignment with incremental improvements over previous versions of the ClustalX and ClustalW-MPI software. The primary advantage of ClustalXeed over other multiple sequence alignment software is its ability to align a large family of protein or nucleic acid sequences. To solve the conventional memory-dependency problem, ClustalXeed uses both physical random access memory (RAM) and a distributed file-allocation system for distance matrix construction and pair-align computation. The computation efficiency of disk-storage system was markedly improved by implementing an efficient load-balancing algorithm, called "idle node-seeking task algorithm" (INSTA). The new editing option and the graphical user interface (GUI) provide ready access to a parallel-computing environment for users who seek fast and easy alignment of large DNA and protein sequence sets.


CONCLUSIONS
ClustalXeed can now compute a large volume of biological sequence data sets, which were not tractable in any other parallel or single MSA program. The main developments include: 1) the ability to tackle larger sequence alignment problems than possible with previous systems through markedly improved storage-handling capabilities. 2) Implementing an efficient task load-balancing algorithm, INSTA, which improves overall processing times for multiple sequence alignment with input sequences of non-uniform length. 3) Support for both single PC and distributed cluster systems.
Kim
Taeho
T
Department of Physiology and Integrated Biosystems, College of Medicine, Inje University, Busan 614-735, South Korea.
Joo
Hyun
H
D000465:Algorithms; D016000:Cluster Analysis; D003205:Computing Methodologies; D016247:Information Storage and Retrieval / Q000379:methods; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface