A space-efficient algorithm for sequence alignment with inversions and reversals

DOI10.1016/J.TCS.2004.02.040MaRDI QIDQ1884840zbMATH OpenOpenAlexFDO

Authors Zhi-Zhong Chen, Yong Gao, Robert Niewiadomski, Yang Wang, Junfeng Wu, Guohui Lin, Yang Wang, Junfeng Wu

Publication date 27 October 2004

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.tcs.2004.02.040

zbMATH Keywords

Dynamic programmingInversionReversalSequence alignment

Mathematics Subject Classification ID

Dynamic programming (90C39)

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Cites work

• A local algorithm for DNA sequence alignment with inversions
• Algorithms on Strings, Trees and Sequences
• An improved algorithm for sequence comparison with block reversals

Cited in

(17)

• Alignments with non-overlapping moves, inversions and tandem duplications in \(O(n^{4})\) time
• A local algorithm for DNA sequence alignment with inversions
• Block reversal on finite words
• Alignment with non-overlapping inversions and translocations on two strings
• Efficient matching of biological sequences allowing for non-overlapping inversions
• An improved algorithm for sequence comparison with block reversals
• A Space Efficient Algorithm for Sequence Alignment with Inversions
• General space-efficient sampling algorithm for suboptimal alignment
• Alignments with Non-overlapping Moves, Inversions and Tandem Duplications in O(n 4) Time
• Efficient string-matching allowing for non-overlapping inversions
• Non-overlapping inversion on strings and languages
• An efficient algorithm to detect common ancestor genes for non-overlapping inversion and applications
• An efficient algorithm for sequence comparison with block reversals
• Rich words in the block reversal of a word
• Sequence searching allowing for non-overlapping adjacent unbalanced translocations
• A space efficient algorithm for finding the best nonoverlapping alignment score
• Efficient algorithms for computing the edit distance with non-overlapping inversions

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