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Complexity Measures for Gene Assembly

Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg, Complexity Measures for Gene Assembly. TUCS Technical Reports 781, Turku Centre for Computer Science, 2006.

Abstract:

The process of gene assembly in ciliates is a fascinating example of
programmed DNA manipulations in living cells. Macronuclear genes are
split into coding blocks (called MDSs), shuffled and separated by
non-coding sequences to form micronuclear genes. Assembling the
coding blocks from micronuclear genes to form functional
macronuclear genes is facilitated by an impressive in-vivo
implementation of the linked list data structure of computer
science. Complexity measures for genes may be defined in many ways,
including the number of MDSs, the number of loci, etc. We take a
different approach in this paper and propose four complexity
measures for genes in ciliates, based on the `effort' required to
assemble the gene. We consider: (a) the types of operations used in
the assembly, (b) the number of operations used in the assembly, (c)
the length of the molecular folds involved, and (d) the length of
the shortest possible parallel assembly for that gene.

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BibTeX entry:

@TECHREPORT{tHaLiPeRo06a,
  title = {Complexity Measures for Gene Assembly},
  author = {Harju, Tero and Li, Chang and Petre, Ion and Rozenberg, Grzegorz},
  number = {781},
  series = {TUCS Technical Reports},
  publisher = {Turku Centre for Computer Science},
  year = {2006},
  keywords = {Gene assembly, complexity measures, weights of operations},
  ISBN = {952-12-1775-8},
}

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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