Document Detail


Bayesian sampling of genomic rearrangement scenarios via double cut and join.
MedLine Citation:
PMID:  21037244     Owner:  NLM     Status:  In-Process    
Abstract/OtherAbstract:
MOTIVATION: When comparing the organization of two genomes, it is important not to draw conclusions on their modes of evolution from a single most parsimonious scenario explaining their differences. Better estimations can be obtained by sampling many different genomic rearrangement scenarios. For this problem, the Double Cut and Join (DCJ) model, while less relevant, is computationally easier than the Hannenhalli-Pevzner (HP) model. Indeed, in some special cases, the total number of DCJ sorting scenarios can be analytically calculated, and uniformly distributed random DCJ scenarios can be drawn in polynomial running time, while the complexity of counting the number of HP scenarios and sampling from the uniform distribution of their space is unknown, and conjectured to be #P-complete. Statistical methods, like Markov chain Monte Carlo (MCMC) for sampling from the uniform distribution of the most parsimonious or the Bayesian distribution of all possible HP scenarios are required.
RESULTS: We use the computational facilities of the DCJ model to draw a sampling of HP scenarios. It is based on a parallel MCMC method that cools down DCJ scenarios to HP scenarios. We introduce two theorems underlying the theoretical mixing properties of this parallel MCMC method. The method was tested on yeast and mammalian genomic data, and allowed us to provide estimates of the different modes of evolution in diverse lineages.
AVAILABILITY: The program implemented in Java 1.5 programming language is available from http://www.renyi.hu/~miklosi/DCJ2HP/.
Authors:
István Miklós; Eric Tannier
Related Documents :
23566734 - Improving risk classification of critical illness with biomarkers: a simulation study.
24619294 - Gps-based microenvironment tracker (microtrac) model to estimate time-location of indiv...
24137664 - Development and validation of an intraoperative predictive model for unplanned postoper...
11191194 - Is modelling dental caries a 'normal' thing to do?
8780354 - Whole-body impedance--what does it measure?
22036684 - Cortical current source estimation from electroencephalography in combination with near...
Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2010-10-29
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  26     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2010 Dec 
Date Detail:
Created Date:  2010-12-02     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  3012-9     Citation Subset:  IM    
Affiliation:
Department of Stochastics, Rényi Institute, Budapest, Hungary. miklosi@renyi.hu
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  Health outcomes in economic evaluation: the QALY and utilities.
Next Document:  Identification of human-specific transcript variants induced by DNA insertions in the human genome.