Flanker: a tool for comparative genomics of gene flanking regions.
antimicrobial resistance (AMR)
bioinformatics
mobile genetic element (MGE)
plasmid
whole-genome sequencing
Journal
Microbial genomics
ISSN: 2057-5858
Titre abrégé: Microb Genom
Pays: England
ID NLM: 101671820
Informations de publication
Date de publication:
09 2021
09 2021
Historique:
entrez:
24
9
2021
pubmed:
25
9
2021
medline:
27
1
2022
Statut:
ppublish
Résumé
Analysing the flanking sequences surrounding genes of interest is often highly relevant to understanding the role of mobile genetic elements (MGEs) in horizontal gene transfer, particular for antimicrobial-resistance genes. Here, we present Flanker, a Python package that performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of MGEs without prior knowledge of their structure. These clusters, known as 'flank patterns' (FPs), are based on Mash distances, allowing for easy comparison of similarity across sequences. Additionally, Flanker can be flexibly parameterized to fine-tune outputs by characterizing upstream and downstream regions separately, and investigating variable lengths of flanking sequence. We apply Flanker to two recent datasets describing plasmid-associated carriage of important carbapenemase genes (
Identifiants
pubmed: 34559044
doi: 10.1099/mgen.0.000634
pmc: PMC8715433
doi:
Substances chimiques
Bacterial Proteins
0
beta-Lactamases
EC 3.5.2.6
carbapenemase
EC 3.5.2.6
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Wellcome Trust
ID : 203141/Z/16/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 220422/Z/20/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/T001151/1
Pays : United Kingdom
Organisme : Department of Health
ID : NIHR200915
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : MRF
ID : MRF_MRF-145-0004-TPG-AVISO
Pays : United Kingdom
Références
Lancet Infect Dis. 2018 Oct;18(10):1138-1149
pubmed: 30126643
Bioinformatics. 2009 Jun 1;25(11):1422-3
pubmed: 19304878
Genome Med. 2014 Nov 20;6(11):90
pubmed: 25422674
Genome Res. 2019 Feb;29(2):304-316
pubmed: 30679308
Nat Commun. 2018 Mar 21;9(1):1179
pubmed: 29563494
Nat Commun. 2022 Mar 3;13(1):1131
pubmed: 35241674
Microb Genom. 2018 Jul;4(7):
pubmed: 29916797
mBio. 2019 Jan 22;10(1):
pubmed: 30670621
Trends Microbiol. 2014 Dec;22(12):686-96
pubmed: 25304194
J Appl Microbiol. 2019 Apr;126(4):1081-1095
pubmed: 30693606
Microb Genom. 2021 May;7(5):
pubmed: 33961543
Antimicrob Agents Chemother. 2014 Jul;58(7):3895-903
pubmed: 24777092
Antimicrob Agents Chemother. 2011 Nov;55(11):5370-3
pubmed: 21844325
Foodborne Pathog Dis. 2019 Jan;16(1):5-22
pubmed: 30418042
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
Nat Microbiol. 2019 Nov;4(11):1919-1929
pubmed: 31358985
Front Microbiol. 2016 Feb 19;7:173
pubmed: 26925045
Genome Med. 2021 Sep 3;13(1):144
pubmed: 34479643
BMJ Open. 2017 Mar 21;7(3):e013665
pubmed: 28325858
Proc Natl Acad Sci U S A. 2020 Oct 6;117(40):25043-25054
pubmed: 32968015
Sci Rep. 2019 Nov 22;9(1):17394
pubmed: 31758048
Microb Genom. 2018 Dec;4(12):
pubmed: 30465646
Microb Genom. 2020 Jan;6(1):
pubmed: 31935184
J Antimicrob Chemother. 2021 Jan 1;76(1):101-109
pubmed: 33009809
Antimicrob Agents Chemother. 2014 Jul;58(7):3785-90
pubmed: 24752261
mBio. 2016 Apr 19;7(2):e02227-15
pubmed: 27094336
FEBS J. 2019 Oct;286(19):3797-3810
pubmed: 31319017
Microb Genom. 2018 Aug;4(8):
pubmed: 30052170
Nat Commun. 2020 May 15;11(1):2452
pubmed: 32415210
Clin Microbiol Rev. 2019 Nov 13;33(1):
pubmed: 31722889
Curr Opin Microbiol. 2018 Oct;45:131-139
pubmed: 29723841
Genome Biol. 2016 Jun 20;17(1):132
pubmed: 27323842
Antimicrob Agents Chemother. 2008 Aug;52(8):2950-4
pubmed: 18519712