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CONSTRAINTS
2008

Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination

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Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination
Aligning DNA and protein sequences is a core technique in molecular biology. Often, it is desirable to include partial prior knowledge and conditions in an alignment. Going beyond prior work, we aim at the integration of such side constraints in free combination into alignment algorithms. The most common and successful technique for efficient alignment algorithms is dynamic programming (DP). However, a weakness of DP is that one cannot include additional constraints without specifically tailoring a new DP algorithm. Here, we discuss a declarative approach that is based on constraint techniques and show how it can be extended by formulating additional knowledge as constraints. We take special care to obtain the efficiency of DP for sequence alignment. This is achieved by careful modeling and applying proper solving strategies. Finally, we apply our method to the scanning for RNA motifs in large sequences. This case study demonstrates how the new approach can be used in real biological ...
Sebastian Will, Anke Busch, Rolf Backofen
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where CONSTRAINTS
Authors Sebastian Will, Anke Busch, Rolf Backofen
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