ClustalXeed, Software download Sites

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

BMC Bioinformatics Article download : http://www.biomedcentral.com/1471-2105/11/467

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...

Taeho Kim, Hyun Joo

The Software Download Site :

http://www.mediafire.com/?thypv8h3dxzc9q1      clustalXeed-1.0.tar.gz (linux version)

http://www.mediafire.com/?7nr42a443ugwmf6   ClustalXeed-Manual-1a.pdf (including installation)


or download both files in a zip format:

http://www.mediafire.com/?4j1af1va86pc66y     
clustalXeed-1.0.tar.gz (linux version) + ClustalXeed-Manual-1a.pdf (including installation)


** The software runs on a Linux OS. For more information, send a mail to : phyjoo@inje.ac.kr

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Clustalxeed-MSA for tons of biological DATA

ClustalXeed - Cloud Computing

       Web source: http://portal.eqentia.com/cloudcomputing/source/13027-BioMed-Central

Timeline of Clustal* Series -Cute and Compressed View

The history of Clustal Series...
[web source: http://www.dipity.com/timeline/Clustalw]

Timeline of Clustal Series

Accurate and Fast MSA tool may accelerate the discovery of mitochondrial DNA mutations

Does strong hypertrophic condition induce fast mitochondrial
DNA mutation of rabbit heart?

Homo- and heteroplasmic mitochondrial DNA (mtDNA) mutations were observed and identified in an isoproterenol-induced rabbit model of cardiac hypertrophy. Genes encoding proteins essential for catalyzing mitochondrial electron transfer and for generating the proton motive force, such as NADH dehydrogenases (ND2, ND3, ND4, and ND6), cytochrome b, and ATPase 8, showed increased susceptibility for mutation. Specifically, five mutations caused amino acid changes and were located in Complex I and Complex V gene clusters. To our knowledge, this is the first demonstration of a relationship between cardiac hypertrophy induced by a strong sympathetic load and rapid mtDNA mutations.

Ref: T. Kim et al. Mitochondrion 8 (2008) 279.283

Application of in silico sequence homology searching

A putative prokaryotic inward rectifier K+ (Kir) channel
was discovered by in silico sequence homology and membrane topology analyses with respect to the number of transmembrane domains (TMs) and the presence of K+ selectivity filter and/or ATP binding sites..

New Kir6.2 Channel Discovered

Ref: The Journal of Microbiology (2010) Vol. 48, No. 3, pp. 325-330

Are you suffer from huge Phylogenetic Tree Drawing?

ClustalXeed provides a scalable vector graphics option for big tree drawing...