Title :
Massive multiple sequence alignment of 16S bacterial ribosomal RNAs using ClustalW-Message Passing Interface (MPI) Based on Beowulf Linux system
Author :
Kim, Hyon Chang ; Seo, Yong Beom ; Song, Ji Hwan ; Choi, Dong Soon ; Min, Churl K. ; Kim, Han Jip
Author_Institution :
Dept. of Biol. Sci., Ajou Univ., Suwon, South Korea
Abstract :
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.
Keywords :
Linux; application program interfaces; biology computing; cellular biophysics; drugs; macromolecules; message passing; microorganisms; organic compounds; AMD Opteron 64 bit microprocessors; Beowulf Linux system; ClustalW-Message Passing Interface; Debian-Beowulf computer cluster; Local Area Multicomputer; bacterial ribosomal RNA; drug targets; multiple sequence alignment; ribosomal antibiotics; Antibiotics; Biology computing; Computer interfaces; Genetic mutations; Linux; Microorganisms; Microprocessors; RNA; Sequences; Switches; 16S ribosomal RNA; ClustalWMPI; multiple sequence alignment; ribosomal antibiotics;
Conference_Titel :
Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE
Print_ISBN :
0-7695-2442-7
DOI :
10.1109/CSBW.2005.88
