An efficient alignment algorithm for masked sequences

DOI10.1016/J.TCS.2006.10.003MaRDI QIDQ868939zbMATH OpenOpenAlexFDO

Authors Jin Wook Kim, Kunsoo Park

Publication date 26 February 2007

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

Full work available at URL https://doi.org/10.1016/j.tcs.2006.10.003

zbMATH Keywords

affine gap penaltyglobal alignmentlocal alignmentmasked sequence

Mathematics Subject Classification ID

Searching and sorting (68P10) Nonnumerical algorithms (68W05)

Recommendations

• Computing and Combinatorics
• Constrained sequence alignment
• A time-efficient, linar-space local similarity algorithm
• Optimal sequence alignment allowing for long gaps
• Linear-space algorithms that build local alignments from fragments

Cites work

• A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices
• Algorithms on Strings, Trees and Sequences
• scientific article; zbMATH DE number 699389 (Why is no real title available?)

Cited in

(2)

• Computing and Combinatorics
• Computing similarity of run-length encoded strings with affine gap penalty

Describes a project that uses

Uses Software

• ARACHNE
• Phrap
• RePS
• RepeatMasker

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