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P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

Overview of attention for article published in BMC Genomics, March 2018
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (84th percentile)
  • High Attention Score compared to outputs of the same age and source (93rd percentile)

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27 X users

Citations

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51 Mendeley
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Title
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
Published in
BMC Genomics, March 2018
DOI 10.1186/s12864-018-4567-3
Pubmed ID
Authors

Bai-Han Zhu, Jun Xiao, Wei Xue, Gui-Cai Xu, Ming-Yuan Sun, Jiong-Tang Li

Abstract

Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene regions. Genomes are widely transcribed, generating messenger and non-coding RNAs. These widespread transcripts can be used to scaffold genomes and complete transcribed regions. We present P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs. Tested in various species, P_RNA_scaffolder exhibited higher speed and efficiency than the existing state-of-the-art scaffolders. This tool also improved the contiguity of genome assemblies generated by current mate-pair scaffolding and third-generation single-molecule sequencing assembly. The P_RNA_scaffolder can improve the contiguity of genome assembly and benefit gene prediction. This tool is available at http://www.fishbrowser.org/software/P_RNA_scaffolder .

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X Demographics

The data shown below were collected from the profiles of 27 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 51 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 51 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 15 29%
Student > Ph. D. Student 9 18%
Student > Master 6 12%
Other 5 10%
Student > Bachelor 3 6%
Other 5 10%
Unknown 8 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 17 33%
Biochemistry, Genetics and Molecular Biology 13 25%
Medicine and Dentistry 2 4%
Neuroscience 2 4%
Mathematics 1 2%
Other 4 8%
Unknown 12 24%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 14. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 17 April 2023.
All research outputs
#2,391,083
of 24,143,470 outputs
Outputs from BMC Genomics
#674
of 10,916 outputs
Outputs of similar age
#51,092
of 335,125 outputs
Outputs of similar age from BMC Genomics
#14
of 190 outputs
Altmetric has tracked 24,143,470 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 90th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 10,916 research outputs from this source. They receive a mean Attention Score of 4.8. This one has done particularly well, scoring higher than 93% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 335,125 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 84% of its contemporaries.
We're also able to compare this research output to 190 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 93% of its contemporaries.