String-matching and alignment algorithms for finding motifs in NGS data

DOI10.1007/978-3-319-59826-0_11MaRDI QIDQ3305534zbMATH OpenOpenAlexWikidataFDO

Authors G. Fiscon, E. Weitschek

Publication date 7 August 2020

Published in Algorithms for Next-Generation Sequencing Data (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-319-59826-0_11

Mathematics Subject Classification ID

Algorithms on strings (68W32) Protein sequences, DNA sequences (92D20)

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Cites work

• A completeness theorem for Kleene algebras and the algebra of regular events
• A fast string searching algorithm
• A Space-Economical Suffix Tree Construction Algorithm
• Algorithms on Strings, Trees and Sequences
• An introduction to Kolmogorov complexity and its applications
• Efficient randomized pattern-matching algorithms
• Fast Pattern Matching in Strings
• scientific article; zbMATH DE number 1263204 (Why is no real title available?)
• scientific article; zbMATH DE number 1557065 (Why is no real title available?)
• scientific article; zbMATH DE number 828444 (Why is no real title available?)
• Introduction to algorithms
• On-line construction of suffix trees
• Partial-Match Retrieval Algorithms
• Textual data compression in computational biology: algorithmic techniques

Cited in

(7)

• Algorithms for indexing highly similar DNA sequences
• DNA-seq error correction based on substring indices
• Comparative assessment of alignment algorithms for NGS data: features, considerations, implementations, and future
• CUSHAW suite: parallel and efficient algorithms for NGS read alignment
• An efficient approach to merging paired-end reads and incorporation of uncertainties
• An algorithm for mapping short reads to a dynamically changing genomic sequence
• Algorithms for next-generation sequencing data. Techniques, approaches, and applications

Describes a project that uses

Uses Software

• DIALIGN
• Bowtie 2
• BWA
• ClustalW

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