Bounded-length Smith-Waterman alignment

DOI10.4230/LIPICS.WABI.2019.16MaRDI QIDQ5091741zbMATH OpenFDO

Authors Alexander Tiskin

Publication date 27 July 2022

Full work available at URL https://doi.org/10.4230/LIPICS.WABI.2019.16

zbMATH Keywords

local alignmentmatrix searchingsequence alignmentSmith-Waterman alignment

Mathematics Subject Classification ID

Algorithms on strings (68W32) Computational methods for problems pertaining to biology (92-08)

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Cites work

• A CHARACTERIZATION OF THE MONGE PROPERTY AND ITS CONNECTION TO STATISTICS
• A faster algorithm computing string edit distances
• A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices
• Algorithms on Strings, Trees and Sequences
• Classes of cost functions for string edit distance
• Dynamic programming based approximation algorithms for sequence alignment with constraints
• Fast and compact regular expression matching
• Fast distance multiplication of unit-Monge matrices
• Faster subsequence recognition in compressed strings
• Monge properties, discrete convexity and applications
• Parametric optimization of sequence alignment
• Perspectives of Monge properties in optimization
• Semi-local longest common subsequences in subquadratic time
• Semi-local string comparison: algorithmic techniques and applications
• The String-to-String Correction Problem
• The theory and computation of evolutionary distances: Pattern recognition

Cited in

(3)

• APPROXIMATION ALGORITHMS FOR LOCAL ALIGNMENT WITH LENGTH CONSTRAINTS
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