ArticleBioinformatics (Oxford, England)2016
PEP_scaffolder: using (homologous) proteins to scaffold genomes.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed, 16 citations in OpenAlex.
- First draft reference genome and annotation of the alternative oil species Physaria fendleri.G3 (Bethesda, Md.) · 2024Article
- Phylogenomic analyses shed light on the relationships of chiton superfamilies and shell-eye evolution.Marine life science & technology · 2023Article
- Genomic signatures of recent convergent transitions to social life in spiders.Nature communications · 2022Article
- A new species in the major malaria vector complex sheds light on reticulated species evolution.Scientific reports · 2019Article
- Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.Bioinformatics (Oxford, England) · 2019Article
- Genomic insights into neonicotinoid sensitivity in the solitary bee Osmia bicornis.PLoS genetics · 2019Article
- Improving draft genome contiguity with reference-derived in silico mate-pair libraries.GigaScience · 2018Article
- P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads.BMC genomics · 2018Article
- Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins.Science (New York, N.Y.) · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationRecovering the gene structures is one of the important goals of genome assembly. In low-quality assemblies, and even some high-quality assemblies, certain gene regions are still incomplete; thus, novel scaffolding approaches are required to complete gene regions.
resultsWe developed an efficient and fast genome scaffolding method called PEP_scaffolder, using proteins to scaffold genomes. The pipeline aims to recover protein-coding gene structures. We tested the method on human contigs; using human UniProt proteins as guides, the improvement on N50 size was 17% increase with an accuracy of ∼97%. PEP_scaffolder improved the proportion of fully covered proteins among all proteins, which was close to the proportion in the finished genome. The method provided a high accuracy of 91% using orthologs of distant species. Tested on simulated fly contigs, PEP_scaffolder outperformed other scaffolders, with the shortest running time and the highest accuracy. AVAILABILITY AND IMPLEMENTATION: The software is freely available at http://www.fishbrowser.org/software/PEP_scaffolder/ CONTACT: lijt@cafs.ac.cnSupplementary information: Supplementary data are available at Bioinformatics online.
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.