Constrained sequence alignment

DOI10.1007/BF02460648MaRDI QIDQ1209899zbMATHOpenAlexWikidataFDO

Authors Kun-Mao Chao, Ross C. Hardison, Webb Miller

Publication date 16 May 1993

Published in Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/bf02460648

zbMATH Keywords

DNAprotein sequencesaffine gap penaltiesconcave gap penaltiesconstrained sequence alignment

Mathematics Subject Classification ID

Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40) Semi-infinite programming (90C34) Computational methods for problems pertaining to biology (92-08)

Recommendations

• Implementation and Application of Automata
• A fast algorithm for the constrained multiple sequence alignment problem
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Cites work

• A linear space algorithm for computing maximal common subsequences
• A time-efficient, linar-space local similarity algorithm
• Approximate matching of regular expressions
• On the space complexity of some algorithms for sequence comparison
• Sequence comparison with concave weighting functions
• Sparse dynamic programming I
• Speeding up dynamic programming with applications to molecular biology
• The Context Dependent Comparison of Biological Sequences

Cited in

(12)

• An algorithm for the sequence alignment with gap penalty problem using multiway divide-and-conquer and matrix transposition
• An algorithm and applications to sequence alignment with weighted constraints
• Constrained sequence alignment: A general model and the hardness results
• Parametric sequence alignment with constraints
• Global and local sequence alignment with a bounded number of gaps
• Efficient sequence alignment with side-constraints by cluster tree elimination
• An efficient alignment algorithm for masked sequences
• Implementation and Application of Automata
• Linear-space algorithms that build local alignments from fragments
• APPROXIMATION ALGORITHMS FOR LOCAL ALIGNMENT WITH LENGTH CONSTRAINTS
• A fast algorithm for the constrained multiple sequence alignment problem
• Dynamic programming based approximation algorithms for sequence alignment with constraints

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