Massive multiple sequence alignment of 16S bacterial ribosomal RNAs using ClustalW-Message Passing Interface (MPI) Based on Beowulf Linux system

Massive multiple sequence alignment of 16S bacterial ribosomal RNAs using ClustalW-Message Passing Interface (MPI) Based on Beowulf Linux system

We have built a Debian-Beowulf computer cluster consisting of 15 computational nodes, each equipped with 15 AMD Opteron 64 bit microprocessors. Local Area Multicomputer (LAM) - Message Passing Interface (MPI) was used as a portable high-performance implementation for MPI. More than 2,000 bacterial 1...

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Hauptverfasser: Hyon Chang Kim, Yong Beom Seo, Ji Hwan Song, Dong Soon Choi, Min, C.K., Han Jip Kim
Format: Tagungsbericht
Sprache:eng
Schlagworte:
16S ribosomal RNA
Antibiotics
Biology computing
ClustalWMPI
Computer interfaces
Genetic mutations
Linux
Microorganisms
Microprocessors
multiple sequence alignment
ribosomal antibiotics
RNA
Sequences
Switches
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Zusammenfassung:We have built a Debian-Beowulf computer cluster consisting of 15 computational nodes, each equipped with 15 AMD Opteron 64 bit microprocessors. Local Area Multicomputer (LAM) - Message Passing Interface (MPI) was used as a portable high-performance implementation for MPI. More than 2,000 bacterial 16S ribosomal RNAs (rRNAs) were multiply aligned using ClustalW-MPI. Systematic sequence comparison provided several sequences with a very high degree of homology despite their different origins of species. These highly conservative sequences were collected as candidate sequences for drug targets of ribosomal antibiotics.
DOI:10.1109/CSBW.2005.88