New models and algorithms for RNA pseudoknot order assignment

DOI10.34768/AMCS-2020-0024zbMATH Open1466.92138OpenAlexW3083127971MaRDI QIDQ2023637FDOQ2023637

Authors Tomasz Zok, Jan Badura, Sylwester Swat, Kacper Figurski, Mariusz Popenda, Maciej Antczak

Publication date 3 May 2021

Published in International Journal of Applied Mathematics and Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.34768/amcs-2020-0024

zbMATH Keywords

integer programmingmaximum independent setvertex coloringconflict graphRNA pseudoknot order

Mathematics Subject Classification ID

Applications of graph theory (05C90) Linear programming (90C05) Protein sequences, DNA sequences (92D20)

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Cites work

• A Simple Parallel Algorithm for the Maximal Independent Set Problem
• A survey on OR and mathematical methods applied on gene-environment networks
• Algorithm 457: finding all cliques of an undirected graph
• An algorithm to analyze stability of gene-expression patterns
• Building the library of RNA 3D nucleotide conformations using the clustering approach
• DNA sequence assembly involving an acyclic graph model
• Emergent computation. Emphasizing bioinformatics.
• Finding a Maximum Independent Set
• Fuzzy prediction strategies for gene-environment networks -- fuzzy regression analysis for two-modal regulatory systems
• G-MAPSEQ -- a new method for mapping reads to a reference genome
• Graph algorithms for DNA sequencing -- origins, current models and the future
• Modeling, inference and optimization of regulatory networks based on time series data
• Modelling DNA and RNA secondary structures using matrix insertion-deletion systems
• Optimal pathway reconstruction on 3D NMR maps
• Stability analysis of nonlinear time-delayed systems with application to biological models
• Tabu search for the RNA partial degradation problem
• The orderly colored longest path problem -- a survey of applications and new algorithms

Cited in

(6)

• Graph-theoretic partitioning of RNAs and classification of pseudoknots
• scientific article; zbMATH DE number 1953301 (Why is no real title available?)
• Computational Science – ICCS 2005
• Minimal state automata for detecting a \(\beta\) globin gene mutation
• Combinatorial Computational Biology of RNA
• Visualization of RNA secondary structure with pseudoknots

Describes a project that uses

Uses Software

• R-CHIE
• G-MAPSEQ
• Algorithm 457

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