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

fYear

2005

fDate

8-11 Aug. 2005

Firstpage

241

Lastpage

242

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;

fLanguage

English

Publisher

ieee

Conference_Titel

Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE

Print_ISBN

0-7695-2442-7

Type

conf

DOI

10.1109/CSBW.2005.88

Filename

1540614