ArticlePloS one2008
The trouble with sliding windows and the selective pressure in BRCA1.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Topsicle: a method for estimating telomere length from whole genome long-read sequencing data.Genome biology · 2025Article
- Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis.BMC genomics · 2021Article
- DNA damage repair system in C57BL/6 J mice is evolutionarily stable.BMC genomics · 2021Article
- Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana.Molecular biology and evolution · 2019Article
- Cell-Derived Viral Genes Evolve under Stronger Purifying Selection in Rhadinoviruses.Journal of virology · 2018Article
- Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave.BMC genomics · 2018Article
- Diversification of defensins and NLRs in Arabidopsis species by different evolutionary mechanisms.BMC evolutionary biology · 2017Article
- Article
- Genome-wide genetic heterogeneity discovery with categorical covariates.Bioinformatics (Oxford, England) · 2017Article
- Evolutionary Analysis of the Mammalian Tuftelin Sequence Reveals Features of Functional Importance.Journal of molecular evolution · 2017Article
- Population genomic analyses of early-phase Atlantic Salmon (Salmo salar) domestication/captive breeding.Evolutionary applications · 2015Article
- Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance.BMC genomics · 2014Article
- Article
- Synonymous site conservation in the HIV-1 genome.BMC evolutionary biology · 2013Article
- Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions.BMC evolutionary biology · 2012Article
- Evolutionary forces shaping genomic islands of population differentiation in humans.BMC genomics · 2012Article
- Divergence of the yeast transcription factor FZF1 affects sulfite resistance.PLoS genetics · 2012Article
- Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.Genome research · 2011Article
- Detection of lineage-specific evolutionary changes among primate species.BMC bioinformatics · 2011Article
- Selection and the cell cycle: positive Darwinian selection in a well-known DNA damage response pathway.Journal of molecular evolution · 2010Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sliding-window analysis has widely been used to uncover synonymous (silent, d(S)) and nonsynonymous (replacement, d(N)) rate variation along the protein sequence and to detect regions of a protein under selective constraint (indicated by d(N)<d(S)) or positive selection (indicated by d(N)>d(S)). The approach compares two or more protein-coding genes and plots estimates d(/\)(S) and d(/\)(N) from each sliding window along the sequence. Here we demonstrate that the approach produces artifactual trends of synonymous and nonsynonymous rate variation, with greater variation in d(/\)(S) than in d(/\)(N). Such trends are generated even if the true d(S) and d(N) are constant along the whole protein and different codons are evolving independently. Many published tests of negative and positive selection using sliding windows that we have examined appear to be invalid because they fail to correct for multiple testing. Instead, likelihood ratio tests provide a more rigorous framework for detecting signals of natural selection affecting protein evolution. We demonstrate that a previous finding that a particular region of the BRCA1 gene experienced a synonymous rate reduction driven by purifying selection is likely an artifact of the sliding window analysis. We evaluate various sliding-window analyses in molecular evolution, population genetics, and comparative genomics, and argue that the approach is not generally valid if it is not known a priori that a trend exists and if no correction for multiple testing is applied.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.