ArticleGenome research2009
Multiple whole-genome alignments without a reference organism.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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
38 citing papers in PubMed, 78 citations in OpenAlex.
- Quantifying Hierarchical Conflicts in Homology Statements.Journal of molecular evolution · 2025Article
- Multiple genome alignment in the telomere-to-telomere assembly era.Genome biology · 2022Review
- Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs.BMC genomics · 2021Article
- Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ.Nature communications · 2020Article
- Demographic Processes Linked to Genetic Diversity and Positive Selection across a Species' Range.Plant communications · 2020Article
- Whole-Genome Alignment and Comparative Annotation.Annual review of animal biosciences · 2019Review
- Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points.Bioinformatics (Oxford, England) · 2019Article
- Article
- Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor.Molecular biology and evolution · 2016Article
- Ensembl comparative genomics resources.Database : the journal of biological databases and curation · 2016Article
- Article
- Development of Gene-Based SSR Markers in Rice Bean (Vigna umbellata L.) Based on Transcriptome Data.PloS one · 2016Article
- Functionally conserved enhancers with divergent sequences in distant vertebrates.BMC genomics · 2015Article
- Assembly and diploid architecture of an individual human genome via single-molecule technologies.Nature methods · 2015Article
- Split-alignment of genomes finds orthologies more accurately.Genome biology · 2015Article
- An alignment-free method to find and visualise rearrangements between pairs of DNA sequences.Scientific reports · 2015Article
- Alignathon: a competitive assessment of whole-genome alignment methods.Genome research · 2014Article
- GenomeVISTA--an integrated software package for whole-genome alignment and visualization.Bioinformatics (Oxford, England) · 2014Article
- The genome of Eucalyptus grandis.Nature · 2014Article
- Genome alignment with graph data structures: a comparison.BMC bioinformatics · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the last common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and six Drosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families-perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.
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.