Evidence map›Paper›PMID 28056784›Full record

ArticleBMC bioinformatics2017

T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes.

Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L Robertson, Panayotis Markoulatos, Grigoris D Amoutzias

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
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

4 citing papers in PubMed.

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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

7 authors.

Michail TsimpidisDepartment of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece.
Georgios BachoumisDepartment of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece.
Kalliopi MimouliDepartment of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece.
Zaharoula KyriakopoulouDepartment of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece.
David L RobertsonFaculty of Life Sciences, University of Manchester, Manchester, UK.
Panayotis MarkoulatosDepartment of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece.
Grigoris D AmoutziasDepartment of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece. amoutzias@bio.uth.gr.ORCID http://orcid.org/0000-0001-5961-964X

Funding

Medical Research Council MC_UU_12014/12
6 · The paper itself

Abstract

backgroundMany computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequence fragments and detect candidate recombination events that may later be further analyzed with more sensitive and specialized methods.

resultsT-RECs, a Windows based graphical tool, employs pairwise alignment of sliding windows and can perform (i) genotyping, (ii) clustering of new genomes, (iii) detect recent recombination events among different evolutionary lineages, (iv) manual inspection of detected recombination events by similarity plots and (v) annotation of genomic regions.

conclusionsT-RECs is very effective, as demonstrated by an analysis of 555 Norovirus complete genomes and 2500 sequence fragments, where a recombination hotspot was identified at the ORF1-ORF2 junction.

Indexed as

Genome, ViralRecombination, GeneticCluster AnalysisDatabases, GeneticDNA FragmentationDNA, ViralEvolution, MolecularGenotyping TechniquesNorovirusSequence AlignmentSequence Analysis, DNASoftwareDNA, ViralGraphical toolNorovirusPairwise alignmentRecombinationSimilarity plotVirus

Identifiers

PMID28056784
PMCPMC5216575

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Registered trials

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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.