Mbs

Modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection

Kosuke Teshima, Hideki Innan

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

Background: The pattern of single nucleotide polymorphisms, or SNPs, contains a tremendous amount of information with respect to the mechanisms of the micro-evolutionary process of a species. The inference of the roles of these mechanisms, including natural selection, relies heavily on computer simulations. A coalescent simulation is extremely powerful in generating a large number of samples of DNA sequences from a population (species) when all mutations are neutral, and Hudson's ms software is frequently used for this purpose. However, it has been difficult to incorporate natural selection into the coalescent framework. Results: We herein present a software applicationto generate samples of DNA sequences when there is a biallelic site targeted by selection. This software application, referred to as mbs, is developed by modifying Hudson's ms. The mbs software is so flexible that it can incorporate any arbitrary histories of population size changes and any mode of selection as long as selection is operating on a biallelic site. Conclusion: mbs provides opportunities to investigate the effect of any mode of selection on the pattern of SNPs under various demography.

Original languageEnglish
Article number166
JournalBMC bioinformatics
Volume10
DOIs
Publication statusPublished - May 30 2009

Fingerprint

DNA sequences
DNA Sequence
Software
Single Nucleotide Polymorphism
Natural Selection
Genetic Selection
Nucleotides
Polymorphism
Application programs
Demography
Single nucleotide Polymorphism
Computer simulation
Population Density
Population Size
Computer Simulation
Mutation
Arbitrary
Population
Simulation

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Structural Biology
  • Applied Mathematics

Cite this

Mbs : Modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection. / Teshima, Kosuke; Innan, Hideki.

In: BMC bioinformatics, Vol. 10, 166, 30.05.2009.

Research output: Contribution to journalArticle

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