ArticleGenome biology2015
Split-alignment of genomes finds orthologies more accurately.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
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- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
- Further varieties of ancient endogenous retrovirus in human DNA.Mobile DNA · 2025Article
- The origin, evolution, and translocation of sex chromosomes in Silurus catfish mediated by transposons.BMC biology · 2025Article
- Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline.bioRxiv : the preprint server for biology · 2025Article
- A Complete Assembly and Annotation of the American Shad Genome Yields Insights into the Origins of Diadromy.Genome biology and evolution · 2025Article
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- Targeted nanopore sequencing using the Flongle device to identify mitochondrial DNA variants.Scientific reports · 2024Article
- A comprehensive atlas of nuclear sequences of mitochondrial origin (NUMT) inserted into the pig genome.Genetics, selection, evolution : GSE · 2024Article
- Genomes of diverse Actinidia species provide insights into cis-regulatory motifs and genes associated with critical traits.BMC biology · 2024Article
- The black honey bee genome: insights on specific structural elements and a first step towards pangenomes.Genetics, selection, evolution : GSE · 2024Article
- Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae.BMC biology · 2024Article
- Chromosome-level genome assembly of the yeast Lodderomyces beijingensis reveals the genetic nature of metabolic adaptations and identifies subtelomeres as hotspots for amplification of mating type loci.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
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- Extreme genome scrambling in marine planktonicGenome research · 2024Article
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- Evolution and subfamilies of HERVL human endogenous retrovirus.Bioinformatics advances · 2024Article
- Fast and robust metagenomic sequence comparison through sparse chaining with skani.Nature methods · 2023Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a new pair-wise genome alignment method, based on a simple concept of finding an optimal set of local alignments. It gains accuracy by not masking repeats, and by using a statistical model to quantify the (un)ambiguity of each alignment part. Compared to previous animal genome alignments, it aligns thousands of locations differently and with much higher similarity, strongly suggesting that the previous alignments are non-orthologous. The previous methods suffer from an overly-strong assumption of long un-rearranged blocks. The new alignments should help find interesting and unusual features, such as fast-evolving elements and micro-rearrangements, which are confounded by alignment errors.
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