ArticleScientific reports2019
Ultra-fast genome comparison for large-scale genomic experiments.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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
30 citing papers in PubMed.
- Draft hybrid assembly and annotation of the Drosophila palustris and Drosophila subpalustris genomes.G3 (Bethesda, Md.) · 2026Article
- Phased T2T horse and donkey assemblies from a mule reveal peculiar equid centromere evolution.Cell genomics · 2026Article
- Unconventional centromere architectures in Tapirus indicus reveal hotspots for satellite-free centromere formation in Perissodactyla.Communications biology · 2026Article
- The genome assemblies of the Tui chub, Siphateles bicolor, and Arroyo chub, Gila orcuttii.The Journal of heredity · 2026Article
- A haplotype-resolved genome assembly of hexaploid Kentucky-31 tall fescue (Lolium arundinaceum).G3 (Bethesda, Md.) · 2026Article
- Genome sequence assembly and annotation ofNAR genomics and bioinformatics · 2025Article
- Haplotype-resolved genome assembly of 'Manhattan' perennial ryegrass (Lolium perenne L.) and characterization of drought responsive late embryogenesis abundant genes.BMC genomics · 2025Article
- Article
- A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat.Nature genetics · 2025Article
- Chromosome-scale assemblies of three Ormosia species: repetitive sequences distribution and structural rearrangement.GigaScience · 2025Article
- Dispensable genome and segmental duplications drive the genome plasticity inFrontiers in fungal biology · 2025Article
- Identification ofFrontiers in veterinary science · 2025Article
- Genome assembly of a diversity panel of Chenopodium quinoa.Scientific data · 2024Article
- Chromosome-scale pearl millet genomes reveal CLAMT1b as key determinant of strigolactone pattern and Striga susceptibility.Nature communications · 2024Article
- Chromosome-scale assembly of the wild wheat relative Aegilops umbellulata.Scientific data · 2023Article
- Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function.G3 (Bethesda, Md.) · 2023Article
- Article
- Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses.Genes · 2023Review
- Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inGenome research · 2023Article
- Genome-Wide Pathway Exploration of theMicroorganisms · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the last decade, a technological shift in the bioinformatics field has occurred: larger genomes can now be sequenced quickly and cost effectively, resulting in the computational need to efficiently compare large and abundant sequences. Furthermore, detecting conserved similarities across large collections of genomes remains a problem. The size of chromosomes, along with the substantial amount of noise and number of repeats found in DNA sequences (particularly in mammals and plants), leads to a scenario where executing and waiting for complete outputs is both time and resource consuming. Filtering steps, manual examination and annotation, very long execution times and a high demand for computational resources represent a few of the many difficulties faced in large genome comparisons. In this work, we provide a method designed for comparisons of considerable amounts of very long sequences that employs a heuristic algorithm capable of separating noise and repeats from conserved fragments in pairwise genomic comparisons. We provide software implementation that computes in linear time using one core as a minimum and a small, constant memory footprint. The method produces both a previsualization of the comparison and a collection of indices to drastically reduce computational complexity when performing exhaustive comparisons. Last, the method scores the comparison to automate classification of sequences and produces a list of detected synteny blocks to enable new evolutionary studies.
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.