A bit-parallel, general integer-scoring sequence alignment algorithm

DOI10.1007/978-3-642-38905-4_7MaRDI QIDQ4928560zbMATH OpenOpenAlexFDO

Authors Yozen Hernandez, Joshua Loving, G. Benson

Publication date 14 June 2013

Published in Combinatorial Pattern Matching (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-642-38905-4_7

zbMATH Keywords

bit-parallelismglobal sequence alignmentinteger weights

Mathematics Subject Classification ID

Algorithms on strings (68W32)

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Cited in

(8)

• Parallel algorithms for mapping short degenerate and weighted DNA sequences to a reference genome
• LCSk: a refined similarity measure
• A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices
• Aligning flowgrams to DNA sequences
• A path selection approach to global pairwise sequence alignment using integer linear optimization†
• A space efficient algorithm for finding the best nonoverlapping alignment score
• A^*PA2: up to 19 faster exact global alignment
• Simple scalable nucleotic FPGA based short Read aligner for exhaustive search of substitution errors

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