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 pairalign computation. The computation efficiency of disk-storage system was markedly improved by imp...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Taeho Kim, Hyun Joo
• Keywords: Biological Sequence Data, BMCBI 2010, Multiple Sequence Alignment, Sequence Alignment Programs