Efficient sequence alignment with side-constraints by cluster tree elimination

DOI10.1007/S10601-007-9032-XMaRDI QIDQ941669zbMATH OpenOpenAlexFDO

Authors Sebastian Will, Anke Busch, Rolf Backofen

Publication date 2 September 2008

Published in Constraints (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s10601-007-9032-x

zbMATH Keywords

Cluster tree eliminationDynamic programmingSequence alignment

Mathematics Subject Classification ID

Dynamic programming (90C39)

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• Constrained sequence alignment
• Efficient algorithms for regular expression constrained sequence alignment
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Cites work

• AND/OR search spaces for graphical models
• Comparison of biosequences
• Parametric sequence alignment with constraints
• Semiring-based constraint satisfaction and optimization
• Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems
• Unifying tree decompositions for reasoning in graphical models

Cited in

(1)

• CONTRAlign: Discriminative Training for Protein Sequence Alignment

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