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Bioinformatics Advance Access published online on January 18, 2007
Bioinformatics, doi:10.1093/bioinformatics/btl650
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

ProServer: A simple, extensible Perl DAS server

Robert D. Finn , James W. Stalker , David K. Jackson , Eugene Kulesha , Jody Clements and Roger Pettett *

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA.

*To whom correspondence should be addressed. Roger Pettett, E-mail: rmp{at}sanger.ac.uk


  Abstract

Summary: The increasing size and complexity of biological databases has led to a growing trend to federate rather than duplicate them. In order to share data between federated databases, protocols for the exchange mechanism must be developed. One such data exchange protocol that is widely used is the Distributed Annotation System (DAS). For example, DAS has enabled small experimental groups to integrate their data in to the Ensembl genome browser. We have developed ProServer, a simple, lightweight, Perl-based DAS server that does not depend on a separate HTTP server. The ProServer package is easily extensible, allowing data to be served from almost any underlying data model. Recent additions to the DAS protocol have enabled both structure and alignment (sequence and structural) data to be exchanged. ProServer allows both of these data types to be served.

Availability: ProServer can be downloaded from http://www.sanger.ac.uk/proserver/ or CPAN http://search.cpan.org/~rpettett/ . Details on the system requirements and installation of ProServer can be found at http://www.sanger.ac.uk/proserver/ .

Supplementary Materials: DasClientExamples.pdf

Associate Editor: Alfonso Valencia

Received on October 20, 2006; revised on December 11, 2006; accepted on December 18, 2006

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