Evidence map›Paper›PMID 34923956›Full record

ArticleBMC genomics2021

InMut-finder: a software tool for insertion identification in mutagenesis using Nanopore long reads.

Rui Song, Ziyao Wang, Hui Wang, Han Zhang, Xuemeng Wang, Hanh Nguyen, David Holding, Bin Yu, Tom Clemente, Shangang Jia and 1 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.1field-weighted citation impact, top 54% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors at 2 institutions in 2 countries.

Rui SongCollege of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
Ziyao WangCollege of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
Hui WangCollege of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
Han ZhangCollege of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
Xuemeng WangCollege of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
Hanh NguyenDepartment of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, 68588, USA.
David HoldingDepartment of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, 68588, USA.
Bin YuCenter for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
Tom ClementeDepartment of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, 68588, USA.
Shangang JiaCollege of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China. shangang.jia@cau.edu.cn.ORCID http://orcid.org/0000-0002-3306-7637
Chi ZhangCenter for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA. czhang5@unl.edu.
China Agricultural University · CNUniversity of Nebraska–Lincoln · US

Funding

Understand the function of the MOS4-associated complex in microRNA biogenesisR01GM127414 · NIGMS · UNIVERSITY OF NEBRASKA LINCOLN · PI YU, BIN · 2018 to 2022
$1.6M
National Science Foundation Award #OIA-1557417NIGMS NIH HHS R01 GM127414
6 · The paper itself

Abstract

backgroundBiological mutagens (such as transposon) with sequences inserted, play a crucial role to link observed phenotype and genotype in reverse genetic studies. For this reason, accurate and efficient software tools for identifying insertion sites based on the analysis of sequencing reads are desired.

resultsWe developed a bioinformatics tool, a Finder, to identify genome-wide Insertions in Mutagenesis (named as "InMut-Finder"), based on target sequences and flanking sequences from long reads, such as Oxford Nanopore Sequencing. InMut-Finder succeeded in identify > 100 insertion sites in Medicago truncatula and soybean mutants based on sequencing reads of whole-genome DNA or enriched insertion-site DNA fragments. Insertion sites discovered by InMut-Finder were validated by PCR experiments.

conclusionInMut-Finder is a comprehensive and powerful tool for automated insertion detection from Nanopore long reads. The simplicity, efficiency, and flexibility of InMut-Finder make it a valuable tool for functional genomics and forward and reverse genetics. InMut-Finder was implemented with Perl, R, and Shell scripts, which are independent of the OS. The source code and instructions can be accessed at https://github.com/jsg200830/InMut-Finder .

Indexed as

NanoporesComputational BiologyHigh-Throughput Nucleotide SequencingMutagenesisSoftware

Identifiers

PMID34923956
PMCPMC8684674
OpenAlexW4200430179

What OpenQuestion holds

Textmetadata
LicenceCC BY
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Registered trials

None linked

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.