Inverse Sequence Alignment from Partial Examples

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Inverse Sequence Alignment from Partial Examples
When aligning biological sequences, the choice of parameter values for the alignment scoring function is critical. Small changes in gap penalties, for example, can yield radically different alignments. A rigorous way to compute parameter values that are appropriate for biological sequences is inverse parametric sequence alignment. Given a collection of examples of biologically correct alignments, this is the problem of finding parameter values that make the example alignments score close to optimal. We extend prior work on inverse alignment to partial examples and to an improved model based on minimizing the average error of the examples. Experiments on benchmark biological alignments show we can find parameters that generalize across protein families and that boost the recovery rate for multiple sequence alignment by up to 25%.
Eagu Kim, John D. Kececioglu
Added 09 Jun 2010
Updated 09 Jun 2010
Type Conference
Year 2007
Where WABI
Authors Eagu Kim, John D. Kececioglu
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