Estimation of Gene Insertion/Deletion Rates with Missing Data Journal Articles

abstract

• AbstractLateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modeled in a maximum-likelihood framework with the additional flexibility of modeling potential missing data. The performance of the models is illustrated using simulations and a data set on gene family phyletic patterns from Gardnerella vaginalis that includes an ancient taxon. A novel application involving pseudogenization/genome reduction magnitudes is also illustrated, using gene family data from Mycobacterium spp. Finally, an R package called indelmiss is available from the Comprehensive R Archive Network at https://cran.r-project.org/package=indelmiss, with support documentation and examples.

authors

• Dang, Utkarsh J
• Devault, Alison M
• Mortimer, Tatum D
• Pepperell, Caitlin S
• Poinar, Hendrik
• Golding, Brian

status

• published 

publication date

• October 1, 2016

has subject area

• 0604 Genetics (FoR)
• Data Interpretation, Statistical (MeSH)
• Developmental Biology (Science Metrix)
• Evolution, Molecular (MeSH)
• Gardnerella vaginalis (MeSH)
• Gene Transfer, Horizontal (MeSH)
• Genome, Bacterial (MeSH)
• INDEL Mutation (MeSH)
• Mutagenesis, Insertional (MeSH)
• Mutation Rate (MeSH)
• Mycobacterium (MeSH)

published in

• Genetics  Journal

keywords

• Data Interpretation, Statistical
• Evolution, Molecular
• Gardnerella vaginalis
• Gene Transfer, Horizontal
• Genome, Bacterial
• INDEL Mutation
• Mutagenesis, Insertional
• Mutation Rate
• Mycobacterium
• gene insertion/deletion
• indel rates
• maximum likelihood
• unobserved data

Digital Object Identifier (DOI)

• 10.1534/genetics.116.191973

start page

• 513

end page

• 529

volume

• 204

issue

• 2