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Bioinformatics Advance Access originally published online on April 29, 2004
Bioinformatics 2004 20(15):2455-2457; doi:10.1093/bioinformatics/bth243
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Bioinformatics 20(15) © Oxford University Press 2004; all rights reserved.

Applications Note

YAdumper: extracting and translating large information volumes from relational databases to structured flat files

José M. Fernández * and Alfonso Valencia

Protein Design Group, National Center for Biotechnology, CNB-CSIC Cantoblanco, Madrid 28049, Spain

Received on July 14, 2003; revised on February 2, 2004; accepted on March 17, 2004
Advance Access Publication April 29, 2004

Summary: Downloading the information stored in relational databases into XML and other flat formats is a common task in bioinformatics. This periodical dumping of information requires considerable CPU time, disk and memory resources. YAdumper has been developed as a purpose-specific tool to deal with the integral structured information download of relational databases. YAdumper is a Java application that organizes database extraction following an XML template based on an external Document Type Declaration. Compared with other non-native alternatives, YAdumper substantially reduces memory requirements and considerably improves writing performance.

Availability: YAdumper is freely available.

Contact: jmfernandez{at}cnb.uam.es

* To whom correspondence should be addressed.


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