APAT ,Automated Protein Annotation Tool. We have determined that the output can be described using one of 6 forms of data: numeric or textual annotation of residues, domains (residue ranges) or whole sequences. A tool may produce a combination of such outputs. With this in mind, an XML data-type definition (DTD) was designed to store the output of any server (`Automated Protein Annotation Tool Markup Language’, APATML).
APAT lets you write simple wrappers for annotation servers which then generate APATML as output. Our display program will then format that as HTML (including colouring of residues and graphs) for you to view, or you may write your own programs to extract and analyze the data.
S.V.V. Deevi , Dr. Andrew C.R. Martin
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S. Vishnu V. Deevi Andrew C. R. Martin
An extensible automated protein annotation tool: standardizing input and output using validated XML