ArticleBMC bioinformatics2005
Evolutionary distance estimation and fidelity of pair wise sequence alignment.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes.BMC bioinformatics · 2025Article
- Molecular genetics, neuroimaging outcomes, and structural analyses of novel and recurrent variants of WDR62 gene in two consanguineous Pakistani families with autosomal recessive primary microcephaly.Molecular biology reports · 2024Article
- Functional annotation of a divergent genome using sequence and structure-based similarity.BMC genomics · 2024Article
- Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter.Molecular biology and evolution · 2019Article
- Impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (PRRSV).BMC veterinary research · 2019Article
- A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity.NPJ biofilms and microbiomes · 2016Article
- Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters.PloS one · 2015Article
- Genetic diversity and recombination analysis in the coat protein gene of Banana bract mosaic virus.Virus genes · 2014Article
- Article
- A multi-platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw (Ara macao).PloS one · 2013Article
- The molecular diversity and evolution of Rice tungro bacilliform virus from Indian perspective.Virus genes · 2012Article
- Genetic variation of coat protein gene among the isolates of Rice tungro spherical virus from tungro-endemic states of the India.Virus genes · 2012Article
- Accounting for alignment uncertainty in phylogenomics.PloS one · 2012Article
- Phylogenetic assessment of alignments reveals neglected tree signal in gaps.Genome biology · 2010Article
- PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins.Plant physiology · 2007Article
- MySSP: non-stationary evolutionary sequence simulation, including indels.Evolutionary bioinformatics online · 2007Article
- New methods for inferring population dynamics from microbial sequences.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2007Review
- The accuracy of several multiple sequence alignment programs for proteins.BMC bioinformatics · 2006Article
- Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments.BMC bioinformatics · 2006Article
- SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent.Nucleic acids research · 2006Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEvolutionary distances are a critical measure in comparative genomics and molecular evolutionary biology. A simulation study was used to examine the effect of alignment accuracy of DNA sequences on evolutionary distance estimation.
resultsUnder the studied conditions, distance estimation was relatively unaffected by alignment error (50% or more of the sites incorrectly aligned) as long as 50% or more of the sites were identical among the sequences (observed P-distance < 0.5). Beyond this threshold, the alignment procedure artificially inflates the apparent sequence identity, skewing distance estimates, and creating alignments that are essentially indistinguishable from random data. This general result was independent of substitution model, sequence length, and insertion and deletion size and rate.
conclusionExamination of the estimated sequence identity may yield some guidance as to the accuracy of the alignment. Inaccurate alignments are expected to have large effects on analyses dependent on site specificity, but analyses that depend on evolutionary distance may be somewhat robust to alignment error as long as fewer than half of the sites have diverged.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.