The estimation of the number and the length distribution of gene conversion tracts from population DNA sequence data

DNA sequence variation studies report the transfer of small segments of DNA among different sequences caused by gene conversion events. Here, we provide an algorithm to detect gene conversion tracts and a statistical model to estimate the number and the length distribution of conversion tracts for p...

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Bibliographic Details
Published in:Genetics (Austin) 1997-05, Vol.146 (1), p.89-99
Main Authors: Betran, E. (Universitat Autonoma de Barcelona, Barcelona, Spain.), Rozas, J, Navarro, A, Barbadilla, A
Format: Article
Language:English
Subjects:
Algorithms
Animals
APLICACIONES DEL ORDENADOR
APPLICATION DES ORDINATEURS
Base Sequence
COMPUTER APPLICATIONS
COMPUTER SIMULATION
Deoxyribonucleic acid
DNA
Drosophila - genetics
Drosophila Proteins
DROSOPHILA SUBOBSCURA
GENE
Gene Conversion
GENES
Genetics
Insect Proteins - genetics
Investigations
LARGURA
LENGTH
LOCI
LOCUS
LONGUEUR
MATEMATICAS
MATHEMATICAL MODELS
MATHEMATICS
MATHEMATIQUE
MAXIMUM LIKELIHOOD
METHODE STATISTIQUE
METODOS ESTADISTICOS
MODELE MATHEMATIQUE
MODELOS MATEMATICOS
Models, Genetic
Molecular Sequence Data
NUCLEOTIDE SEQUENCE
Polymorphism, Genetic
PROBABILITY
Ribosomal Proteins
RP49 LOCUS
SECUENCIA NUCLEOTIDICA
SEQUENCE NUCLEOTIDIQUE
SIMULACION
SIMULATION
Statistical analysis
STATISTICAL METHODS
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Description
Summary:DNA sequence variation studies report the transfer of small segments of DNA among different sequences caused by gene conversion events. Here, we provide an algorithm to detect gene conversion tracts and a statistical model to estimate the number and the length distribution of conversion tracts for population DNA sequence data. Two length distributions are defined in the model: (1) that of the observed tract lengths and (2) that of the true tract lengths. If the latter follows a geometric distribution, the relationship between both distributions depends on two basic parameters: psi, which measures the probability of detecting a converted site, and phi, the parameter of the geometric distribution, from which the average true tract length, 1/(1-phi), can be estimated. Expressions are provided for estimating phi by the method of the moments and that of the maximum likelihood. The robustness of the model is examined by computer simulation. The present methods have been applied to the published rp49 sequences of Drosophila subobscura. Maximum likelihood estimate of phi for this data set is 0.9918, which represents an average conversion tract length of 122 bp. Only a small percentage of extant conversion events is detected.
ISSN:0016-6731
1943-2631
1943-2631
DOI:10.1093/genetics/146.1.89