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Bioinformatics Advance Access originally published online on December 8, 2005
Bioinformatics 2006 22(3):291-296; doi:10.1093/bioinformatics/bti808
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

An extensible automated protein annotation tool: standardizing input and output using validated XML

S. Vishnu V. Deevi 1 and Andrew C. R. Martin 2,*

1School of Animal and Microbial Sciences, The University of Reading P.O. Box 228, Whiteknights, Reading RG6 6AJ, UK
2Department of Biochemistry and Molecular Biology, University College London Gower Street, London WC1E 6BT, UK

*To whom correspondence should be addressed.

Motivation: There is a frequent need to apply a large range of local or remote prediction and annotation tools to one or more sequences. We have created a tool able to dispatch one or more sequences to assorted services by defining a consistent XML format for data and annotations.

Results: By analyzing annotation tools, we have determined that annotations can be described using one or more of the six forms of data: numeric or textual annotation of residues, domains (residue ranges) or whole sequences. With this in mind, XML DTDs have been designed to store the input and output of any server. Plug-in wrappers to a number of services have been written which are called from a master script. The resulting APATML is then formatted for display in HTML. Alternatively further tools may be written to perform post-analysis.

Availability: The ‘Automated Protein Annotation Tool’ (APAT) can be downloaded from http://www.bioinf.org.uk/apat/. As well as source code and documentation, a demonstration web server is provided which uses APAT to perform a number of annotations of a sequence.

Contact: andrew{at}bioinf.org.uk; martin{at}biochem.ucl.ac.uk

Received on July 25, 2005; revised on November 15, 2005; accepted on November 30, 2005

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