Warning: strtotime(): It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected the timezone 'UTC' for now, but please set date.timezone to select your timezone. in /var/www/html/www_publications/index.php on line 342

Warning: Cannot modify header information - headers already sent by (output started at /var/www/html/www_publications/index.php:342) in /var/www/html/www_publications/index.php on line 4076
Simple Operations for Gene Assembly (bibtex)
Simple Operations for Gene Assembly (bibtex)
by Harju, Tero, Petre, Ion, Rogojin, Vladimir and Rozenberg, Grzegorz
Abstract:
The intramolecular model for gene assembly in ciliates considers three operations, $mld$, $mhi$, and $mdlad$ that can assemble any gene pattern through folding and recombination: the molecule is folded so that two occurrences of a pointer (short nucleotide sequence) get aligned and then the sequence is rearranged through recombination of pointers. In general, the sequence rearranged by one operation can be arbitrarily long and consist of many coding and non-coding blocks. We consider in this paper simple variants of the three operations, where only one coding block is rearranged at a time. We characterize in this paper the gene patterns that can be assembled through these variants. Our characterization is in terms of signed permutations and dependency graphs. Interestingly, we show that simple assemblies possess rather involved properties: a gene pattern may have both successful and unsuccessful assemblies and also more than one successful assembling strategy.
Reference:
Simple Operations for Gene Assembly (Harju, Tero, Petre, Ion, Rogojin, Vladimir and Rozenberg, Grzegorz), Technical report 757, , 2006.
Bibtex Entry:
@TechReport{t147,
  author   = {Harju, Tero AND Petre, Ion AND Rogojin, Vladimir AND Rozenberg, Grzegorz},
  title    = {Simple Operations for Gene Assembly},
  year     = {2006},
  number   = {757},
  abstract = {The intramolecular model for gene assembly in ciliates considers three operations, $mld$, $mhi$, and $mdlad$ that can assemble any gene pattern through folding and recombination: the molecule is folded so that two occurrences of a pointer (short nucleotide sequence) get aligned and then the sequence is rearranged through recombination of pointers. In general, the sequence rearranged by one operation can be arbitrarily long and consist of many coding and non-coding blocks. We consider in this paper simple variants of the three operations, where only one coding block is rearranged at a time. We characterize in this paper the gene patterns that can be assembled through these variants. Our characterization is in terms of signed permutations and dependency graphs. Interestingly, we show that simple assemblies possess rather involved properties: a gene pattern may have both successful and unsuccessful assemblies and also more than one successful assembling strategy.},
  keywords = {gene assembly, simple operations, signed permutations, sorting},
  pdf      = {pdfs/HPRG2006a.pdf},
}
Powered by bibtexbrowser