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

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.