ClustalW-MPI: ClustalW analysis using distributed and parallel computing

ClustalW is a tool for aligning multiple protein or nucleotide sequences. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is a distributed and parallel implementation of ClustalW. All three steps have been parallelized to r...

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Vydáno v:Bioinformatics Ročník 19; číslo 12; s. 1585 - 1586
Hlavní autor: Li, Kuo-Bin
Médium: Journal Article
Jazyk:angličtina
Vydáno: Oxford Oxford University Press 12.08.2003
Oxford Publishing Limited (England)
Témata:
Amino Acid Sequence
Base Sequence
Biological and medical sciences
Cluster Analysis
Computing Methodologies
Fundamental and applied biological sciences. Psychology
Gene Expression Profiling - methods
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Molecular Sequence Data
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Sequence Analysis, Protein - methods
Sequence Homology, Amino Acid
Sequence Homology, Nucleic Acid
Software
Computer program
Web site
Bioinformatics
Phylogenetic tree
Sequence alignment
Execution time
ISSN:1367-4803, 1460-2059, 1367-4811
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Popis
Shrnutí:ClustalW is a tool for aligning multiple protein or nucleotide sequences. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is a distributed and parallel implementation of ClustalW. All three steps have been parallelized to reduce the execution time. The software uses a message-passing library called MPI (Message Passing Interface) and runs on distributed workstation clusters as well as on traditional parallel computers. Availability:The source codes are written in ISO C and are available at http://www.bii.a-star.edu.sg/software/clustalw-mpi/. An open source implementations of MPI http://www-unix.mcs.anl.gov/mpi/. Contact: kuobin@bii.a-star.edu.sg
Bibliografie:local:191585
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ark:/67375/HXZ-J9FXRZ01-S
PII:1460-2059
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ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btg192