Pacemaker partition identification

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


The universally observed conservation of the distribution of evolution rates across the complete sets of orthologous genes in pairs of related genomes can be explained by the model of the Universal Pacemaker (UPM) of genome evolution. Under UPM, the relative evolutionary rates of all genes remain nearly constant whereas the absolute rates can change arbitrarily. It was shown on several taxa groups spanning the entire tree of life that the UPM model describes the evolutionary process better than the traditional molecular clock model [26][25]. Here we extend this analysis and ask: how many pacemakers are there and which genes are affected by which pacemakers? The answer to this question induces a partition of the gene set such that all the genes in one part are affected by the same pacemaker. The input to the problem comes with arbitrary amount of statistical noise, hindering the solution even more. In this work we devise a novel heuristic procedure, relying on statistical and geometrical tools, to solve the pacemaker partition identification problem and demonstrate by simulation that this approach can cope satisfactorily with considerable noise and realistic problem sizes. We applied this procedure to a set of over 2000 genes in 100 prokaryotes and demonstrated the significant existence of two pacemakers.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 14th International Workshop, WABI 2014, Proceedings
PublisherSpringer Verlag
Number of pages15
ISBN (Print)9783662447529
StatePublished - 2014
Event14th International Workshop on Algorithms in Bioinformatics, WABI 2014 - Wroclaw, Poland
Duration: 8 Sep 201410 Sep 2014

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume8701 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference14th International Workshop on Algorithms in Bioinformatics, WABI 2014


  • Deming regression
  • Gap Statistics
  • Genome Evolution Pacemaker
  • Molecular Evolution
  • Partition Distance

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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