Assigning Function to CDS Through Qualified Query Answering: Beyond Alignment and Motifs

Terry Gaasterland, Natalia Maltsev, Jorge Logo, and Guo-Hua Chen

In this paper, we show how to use qualitative query answering to annotate CDS-to-function relationships with confidence in the score, confidence in the tool, and confidence in the decision about the function. The system, implemented in Prolog, provides users with a powerful tool to analyze large quantities of data that have been produced by multiple sequence analysis programs. Using qualified query answering techniques, users can easily change the criteria for how tools reinforce each other and for how numbers of occurrences of particular functions reinforce each other. They can also alter how different scores for different tools are categorized.

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