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Bioinformatics Advance Access originally published online on January 5, 2006
Bioinformatics 2006 22(5):618-620; doi:10.1093/bioinformatics/btk020
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
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ANDY: a general, fault-tolerant tool for database searching on computer clusters

Andrew Smith 1,2,3,4, John-Marc Chandonia 2 and Steven E. Brenner 1,2,*

1Department of Plant and Microbial Biology 461A Koshland Hall University of California Berkeley, CA 94720-3102, USA
2Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA
3Department of Molecular Biophysics and Biochemistry, Yale University New Haven, CT 06520, USA
4Department of Computer Science, Yale University New Haven, CT 06520, USA

*To whom correspondence should be addressed.

Summary: ANDY (seArch coordination aND analYsis) is a set of Perl programs and modules for distributing large biological database searches, and in general any sequence of commands, across the nodes of a Linux computer cluster. ANDY is compatible with several commonly used distributed resource management (DRM) systems, and it can be easily extended to new DRMs. A distinctive feature of ANDY is the choice of either dedicated or fair-use operation: ANDY is almost as efficient as single-purpose tools that require a dedicated cluster, but it runs on a general-purpose cluster along with any other jobs scheduled by a DRM. Other features include communication through named pipes for performance, flexible customizable routines for error-checking and summarizing results, and multiple fault-tolerance mechanisms.

Availability: ANDY is freely available and can be obtained from http://compbio.berkeley.edu/proj/andy

Contact: brenner{at}compbio.berkeley.edu

Supplementary information: Supplemental data, figures, and a more detailed overview of the software are found at http://compbio.berkeley.edu/proj/andy

Received on August 22, 2005; revised on November 29, 2005; accepted on December 20, 2005

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