minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data.

Kian Soon Hoon, Deborah C Holt, Sarah Auburn, Peter Shaw, Philip M Giffard

Open access · goldAbstract read

In one paragraph

Article in PeerJ, 2023. 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

–field-weighted citation impact, top 76% 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, 0 citations in OpenAlex.

SNPoptimizer: a scalable genetic-algorithm framework to derive minimal discriminatory SNP panels from large genotyping datasets.Molecular breeding : new strategies in plant improvement · 2026
Article

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

5 authors at 3 institutions in 3 countries.

Kian Soon HoonMenzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

Deborah C HoltMenzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

Sarah AuburnMenzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

Peter ShawOujian Laboratory, Wenzhou, Zhejiang, China.

Philip M GiffardMenzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

Charles Darwin University · AUMahidol Oxford Tropical Medicine Research Unit · THMenzies School of Health Research · AU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Here, we present the R package, minSNPs. This is a re-development of a previously described Java application named Minimum SNPs. MinSNPs assembles resolution-optimised sets of single nucleotide polymorphisms (SNPs) from sequence alignments such as genome-wide orthologous SNP matrices. MinSNPs can derive sets of SNPs optimised for discriminating any user-defined combination of sequences from all others. Alternatively, SNP sets may be optimised to determine all sequences from all other sequences,

Indexed as

Polymorphism, Single NucleotideStaphylococcus aureusGenome, MicrobialGenomicsSequence AlignmentGenomeGenome alignmentsMicrobialPlasmodiumResolution optimisedSNP genotypingSNP matricesSNP miningSNPsStaphylococcus

Identifiers

PMID37250706

DOI10.7717/peerj.15339

PMCPMC10224671

OpenAlexW4377986557

What OpenQuestion holds

Textmetadata

LicenceCC BY

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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.