Literature DB >> 1630310

Sequencing errors and molecular evolutionary analysis.

A G Clark1, T S Whittam.   

Abstract

Heuristic approaches were used to quantify the influence that sequencing errors have on estimates of nucleotide diversity, substitution rate, and the construction of genealogies. Error rates of less than 1 nucleotide/kb probably have little affect on conclusions about the evolutionary history of highly polymorphic organisms such as Drosophila and Escherichia coli, but organisms with very low nucleotide diversity, such as humans, require greater sequencing accuracy. A scan of GenBank for corrections of previous errors reveals that sequencing errors are highly nonrandom.

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Year:  1992        PMID: 1630310     DOI: 10.1093/oxfordjournals.molbev.a040756

Source DB:  PubMed          Journal:  Mol Biol Evol        ISSN: 0737-4038            Impact factor:   16.240


  27 in total

1.  Evaluating the impact of post-mortem damage in ancient DNA: a theoretical approach.

Authors:  Martyna Molak; Simon Y W Ho
Journal:  J Mol Evol       Date:  2011-11-20       Impact factor: 2.395

2.  On the comparison of population-level estimates of haplotype and nucleotide diversity: a case study using the gene cox1 in animals.

Authors:  W P Goodall-Copestake; G A Tarling; E J Murphy
Journal:  Heredity (Edinb)       Date:  2012-03-21       Impact factor: 3.821

Review 3.  Phylogenetics of modern birds in the era of genomics.

Authors:  Scott V Edwards; W Bryan Jennings; Andrew M Shedlock
Journal:  Proc Biol Sci       Date:  2005-05-22       Impact factor: 5.349

4.  Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects.

Authors:  Michael Lynch
Journal:  Mol Biol Evol       Date:  2008-08-25       Impact factor: 16.240

5.  Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences.

Authors:  Xiaoming Liu; Taylor J Maxwell; Eric Boerwinkle; Yun-Xin Fu
Journal:  Mol Biol Evol       Date:  2009-03-24       Impact factor: 16.240

6.  Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life.

Authors:  Chris Todd Hittinger; Mark Johnston; John T Tossberg; Antonis Rokas
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-04       Impact factor: 11.205

7.  Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error.

Authors:  Xiaoming Liu; Yun-Xin Fu; Taylor J Maxwell; Eric Boerwinkle
Journal:  Genome Res       Date:  2009-12-01       Impact factor: 9.043

8.  Analysis of the quality and utility of random shotgun sequencing at low redundancies.

Authors:  J Bouck; W Miller; J H Gorrell; D Muzny; R A Gibbs
Journal:  Genome Res       Date:  1998-10       Impact factor: 9.043

9.  Taxonomic misidentification in public DNA databases.

Authors:  Rytas Vilgalys
Journal:  New Phytol       Date:  2003-10       Impact factor: 10.151

10.  Accurate and fast methods to estimate the population mutation rate from error prone sequences.

Authors:  Bjarne Knudsen; Michael M Miyamoto
Journal:  BMC Bioinformatics       Date:  2009-08-11       Impact factor: 3.169

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