Parallel implementation and performance characterization of MUSCLE

Multiple sequence alignment is a fundamental and very computationally intensive task in molecular biology. MUSCLE, a new algorithm for creating multiple alignments of protein sequences, achieves a highest rank in accuracy and the fastest speed compared to ClustalW as well as T-Coffee, some widely us...

Full description

Saved in:
Bibliographic Details
Main Authors: Xi Deng, Eric Li, Jiulong Shan, Wenguang Chen
Format: Conference Proceeding
Language:English
Subjects:
Acceleration
Biology computing
Computational biology
Computer science
Concurrent computing
Iterative algorithms
Muscles
Phylogeny
Proteins
Sequences
Online Access:Request full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Multiple sequence alignment is a fundamental and very computationally intensive task in molecular biology. MUSCLE, a new algorithm for creating multiple alignments of protein sequences, achieves a highest rank in accuracy and the fastest speed compared to ClustalW as well as T-Coffee, some widely used tools in multiple sequence alignment. To further accelerate the computations, we present the parallel implementation of MUSCLE in this paper. It is decomposed into several independent modules, which are parallelized with different OpenMP paradigms. We also conduct detailed performance characterization on symmetric multiple processor systems. The experiments show that MUSCLE scales well with the increase of processors, and achieves up to 15./spl times/ speedup on 16-way shared memory multiple processor system.
ISSN:1530-2075
DOI:10.1109/IPDPS.2006.1639616