Synteny plot quality control with SyntenyQC.

Timothy D J Kirkwood, Jack A Connolly, Ee Lui Ang, Huimin Zhao, Eriko Takano, Rainer Breitling

Abstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

6 authors.

Timothy D J KirkwoodManchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M1 7DN, United Kingdom.ORCID 0000-0002-6485-0608

Jack A ConnollyManchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M1 7DN, United Kingdom.ORCID 0000-0003-3643-5578

Ee Lui AngSynthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.ORCID 0000-0002-3070-8056

Huimin ZhaoDepartment of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.ORCID 0000-0002-9069-6739

Eriko TakanoManchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M1 7DN, United Kingdom.ORCID 0000-0002-6791-3256

Rainer BreitlingManchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M1 7DN, United Kingdom.ORCID 0000-0001-7173-0922

Funding

A Scalable Platform to Discover Antimicrobials of Ribosomal OriginR01AI144967 · NIAID · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI Douglas Alan Mitchell, WILFRED A. VAN DER DONK · 2019 to 2026

$6.0M

National Research FoundationNational Science Foundation ChE-2019897National Science Foundation DBI-2400058National Science Foundation OISE-2435374NIAID NIH HHS R01 AI144967NIH HHS AI144967

6 · The paper itself

Abstract

summarySyntenyQC is a data pre-processing tool for the construction of synteny plots. It supports genomic data collection, annotation and dereplication to facilitate (and in some cases fundamentally enable) the construction of informative synteny plots. AVAILABILITY AND IMPLEMENTATION: SyntenyQC is a command line app developed using Python version 3.10 and tested using pytest. SyntenyQC is available on PyPI (https://pypi.org/project/SyntenyQC) under the MIT License, along with a detailed user tutorial. Package tests can be viewed at https://github.com/Tim-Kirkwood/SyntenyQC.

Indexed as

GenomicsSoftwareSyntenyMolecular Sequence DataMultigene FamilyStreptomyces coelicolor

Identifiers

PMID41233978

DOI10.1093/bioinformatics/btaf626

PMCPMC12721865

What OpenQuestion holds

Textmetadata

LicenceCC BY

Read underepoch 390

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.