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

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6 Author(s)
Hyon Chang Kim ; Dept. of Biol. Sci., Ajou Univ., Suwon, South Korea ; Yong Beom Seo ; Ji Hwan Song ; Dong Soon Choi
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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.

Published in:

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

Date of Conference:

8-11 Aug. 2005