Alternative splicing is a key process in post-transcriptional regulation, by which several kinds of mature RNA can be obtained from the same premessenger RNA. The resulting combinatorial complexity contributes to biological diversity, especially in the case of the human immunode ciency virus HIV-1. Using a constraint programming approach, we develop a model of the alternative splicing regulation in HIV-1. Our model integrates different scales (single site vs. multiple sites), and thus allows us to exploit several types of experimental data available to us.
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