On computing all suboptimal alignments
DOI10.1016/S0020-0255(97)10032-9zbMATH Open0944.92007OpenAlexW2012143472MaRDI QIDQ1291563FDOQ1291563
Authors: Kun-Mao Chao 
Publication date: 20 September 2000
Published in: Information Sciences (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1016/s0020-0255(97)10032-9
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divide-and-conquersequence comparisonlinear-space algorithmminimal directed acyclic graphsuboptimal alignments
Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40) Dynamic programming (90C39) Parallel algorithms in computer science (68W10) Computational methods for problems pertaining to biology (92-08)
Cites Work
- Efficient string matching
- Efficient Parallel Algorithms for String Editing and Related Problems
- A linear space algorithm for computing maximal common subsequences
- The Multiple Sequence Alignment Problem in Biology
- Approximate matching of regular expressions
- Trees, Stars, and Multiple Biological Sequence Alignment
- A dynamic programming algorithm to find all solutions in a neighborhood of the optimum
- Optimized homology searches of the gene and protein sequence data banks
- Linear-space algorithms that build local alignments from fragments
Cited In (6)
- A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices
- A versatile divide and conquer technique for optimal string alignment
- Computing alignments with maximum synchronous moves via replay in coordinate planes
- General space-efficient sampling algorithm for suboptimal alignment
- Finding a length-constrained maximum-density path in a tree
- Enumerating \(K\) best paths in length order in DAGs
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