Paper Info
Title
Sequence analysis on a 216-processor beowulf cluster
Abstract
In this work we describe the implementation of a 216-processor Beowulf cluster with switched gigabit Ethernet networking. This design includes the use of a 8-CPU high performance midrange computer with 8 gigabit ports as a cluster head, a design that limits I/O contention. We have been developing applications software for bioinformatics research in protein folding, as well as the MoBiDiCK system for managing cluster applications that is extensible to general purpose distributed computing. In addition to the cluster architecture, we present a new cluster application for bioinformatics, a variant of the BLAST family of sequence comparison programs. MOBLAST performs the BLAST algorithm in an exhaustive manner, avoiding its initial heuristic approach to finding hits. This effectively slows BLAST down to approach the speed of other comprehensive search methods such as a Smith-Waterman alignment. MOBLAST requires a sizeable cluster to run. We describe the development of MOBLAST and its use in making an exhaustive M×N database of alignments where M is the set of protein sequences with known 3-D structures, and N is the set of all protein sequences. This M×N database of protein alignments will facilitate further research in protein folding, the ultimate aim of our work with Beowulf cluster technology. Furthermore, we describe a general algorithm for partitioning M×N problems and implement this in the MoBiDiCK computing model.
Year
Venue
Keywords
2000
Annual Linux Showcase & Conference
216-processor beowulf cluster,beowulf cluster technology,protein folding,sizeable cluster,cluster head,cluster application,n database,sequence analysis,protein sequence,cluster architecture,new cluster application,computer model,generic algorithm,distributed computing
Field
DocType
Citations 
Gigabit,Heuristic,General purpose,General algorithm,Computer science,Parallel computing,Software,Gigabit Ethernet,Extensibility,Sequence analysis
Conference
1
PageRank 
References 
Authors
0.79
1
3
Name
Order
Citations
PageRank
Katerina Michalickova119018.67
Moyez Dharsee252.04
Christopher W. V. Hogue31716243.52