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

Deevi, S. V. V. and Martin, A. C. R. (2006) An extensible automated protein annotation tool: standardizing input and output using validated XML. Bioinformatics, 22 (3). pp. 291-296. ISSN 1367-4803

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To link to this item DOI: 10.1093/bioinformatics/bti808

Abstract/Summary

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.

Item Type:Article
Refereed:Yes
Divisions:Faculty of Life Sciences > School of Biological Sciences
ID Code:10149
Uncontrolled Keywords:SUBCELLULAR-LOCALIZATION, SUPPLEMENT TREMBL, SEQUENCE, DATABASE, PREDICTION, INTEGRATION, PROGRAMS, DOMAINS, SERVER, SITES

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