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Bioinformatics Vol. 16 no. 7 2000
Pages 606-612
© 2000 Oxford University Press

Original Paper

Clustalnet: the joining of Clustal and CORBA

F. Campagne 1

1 Department of Physiology and Biophysics, Box 1218, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY 10029-6574, USA

Received on August 24, 1999 ; revised on December 14, 1999 ; accepted on January 28, 2000

Motivation: Performing sequence alignment operations from a different program than the original sequence alignment code, and/or through a network connection, is often required. Interactive alignment editors and large-scale biological data analysis are common examples where such a flexibility is important. Interoperability between the alignment engine and the client should be obtained regardless of the architectures and programming languages of the server and client.

Results: Clustalnet, a Clustal alignment CORBA server is described, which was developed on the basis of Clustalw. This server brings the robustness of the algorithms and implementations of Clustal to a new level of reuse. A Clustalnet server object can be accessed from a program, transparently through the network. We present interfaces to perform the alignment operations and to control these operations via immutable contexts. The interfaces that select the contexts do not depend on the nature of the operation to be performed, making the design modular. The IDL interfaces presented here are not specific to Clustal and can be implemented on top of different sequence alignment algorithm implementations.

Availability: This implementation is freely available for non-commercial use for a variety of architectures. Clustalnet can be downloaded from http://transport.physbio.mssm.edu/clustalnet.

Contact: campagne{at}inka.mssm.edu

Supplementary Information: Alignment encoding description and full IDL in the documentation, with the distribution.


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