Combining overlap and containment for gene assembly in ciliates

DOI10.1016/J.TCS.2009.07.047MaRDI QIDQ847668zbMATH OpenOpenAlexFDO

Authors Robert Brijder, Hendrik Jan Hoogeboom

Publication date 19 February 2010

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

Full work available at URL https://doi.org/10.1016/j.tcs.2009.07.047

zbMATH Keywords

overlap graphgene assembly in ciliatesgraph rewritingDNA transformation

Mathematics Subject Classification ID

Graph theory (including graph drawing) in computer science (68R10) Grammars and rewriting systems (68Q42)

Recommendations

• Extending the Overlap Graph for Gene Assembly in Ciliates
• Simple gene assembly as a rewriting of directed overlap-inclusion graphs
• Extended strings and graphs for simple gene assembly
• Directed overlap-inclusion graphs as representations of ciliate genes
• Aspects of Molecular Computing

Cites work

• scientific article; zbMATH DE number 1836434 (Why is no real title available?)
• A Characterization of Comparability Graphs and of Interval Graphs
• A String-Based Model for Simple Gene Assembly
• A short proof that `proper = unit'
• Characterizing the micronuclear gene patterns in ciliates
• Circle graph obstructions
• Computation in living cells. Gene assembly in ciliates
• Extending the Overlap Graph for Gene Assembly in Ciliates
• Formal systems for gene assembly in ciliates.
• Reducibility of gene patterns in ciliates using the breakpoint graph.
• Representation of a finite graph by a set of intervals on the real line
• Sequential vs. Parallel complexity in simple gene assembly
• Simple gene assembly is deterministic
• Simultaneous representation of interval and interval-containment orders
• String and graph reduction systems for gene assembly in ciliates

Cited in

(6)

• Simple gene assembly as a rewriting of directed overlap-inclusion graphs
• Aspects of Molecular Computing
• Directed overlap-inclusion graphs as representations of ciliate genes
• Extending the Overlap Graph for Gene Assembly in Ciliates
• REDUCTION GRAPHS FROM OVERLAP GRAPHS FOR GENE ASSEMBLY IN CILIATES
• Overlapping genes in vertebrate genomes

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