A study of computational genome assembly by graph theory

DOI10.2478/AWUTM-2024-0001MaRDI QIDQ6494182zbMATH OpenFDO

Authors Bijan Sarkar

Publication date 29 April 2024

Published in Annals of West University of Timisoara - Mathematics and Computer Science (Search for Journal in Brave)

Copyright license Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported

Full work available at URL https://doi.org/10.2478/AWUTM-2024-0001

zbMATH Keywords

bidirectional bipartite graphsde Bruijn graphsde novo assemblygenome assemblySpades assemblerVelvet assembler

Mathematics Subject Classification ID

Coloring of graphs and hypergraphs (05C15) Graph theory (05Cxx) Mathematical aspects of software engineering (specification, verification, metrics, requirements, etc.) (68N30) Biologically inspired models of computation (DNA computing, membrane computing, etc.) (68Q07) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20)

Recommendations

• Graph algorithms for DNA sequencing -- origins, current models and the future
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Cites work

• An Eulerian path approach to DNA fragment assembly
• DNA paired fragment assembly using graph theory
• Graph algorithms for DNA sequencing -- origins, current models and the future

Cited in

(1)

• A tale of optimizing the space taken by de Bruijn graphs

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