PANINI : Pangenome Neighbour Identification for Bacterial Populations

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Abudahab , K , Prada , J M , Yang , Z , Bentley , S D , Croucher , N J , Corander , J & Aanensen , D M 2019 , ' PANINI : Pangenome Neighbour Identification for Bacterial Populations ' , Microbial Genomics , vol. 5 , no. 4 , 000220 .

Title: PANINI : Pangenome Neighbour Identification for Bacterial Populations
Author: Abudahab, Khalil; Prada, Joaquin M.; Yang, Zhirong; Bentley, Stephen D.; Croucher, Nicholas J.; Corander, Jukka; Aanensen, David M.
Contributor organization: Helsinki Institute for Information Technology
Department of Mathematics and Statistics
Jukka Corander / Principal Investigator
Biostatistics Helsinki
Date: 2019-04
Language: eng
Number of pages: 10
Belongs to series: Microbial Genomics
ISSN: 2057-5858
Abstract: The standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here, we introduce PANINI (Pangenome Neighbour Identification for Bacterial Populations), a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding based on the t-SNE (t-distributed stochastic neighbour embedding) algorithm. PANINI is browser-based and integrates with the Microreact platform for rapid online visualization and exploration of both core and accessory genome evolutionary signals, together with relevant epidemiological, geographical, temporal and other metadata. Several case studies with single- and multi-clone pneumococcal populations are presented to demonstrate the ability to identify biologically important signals from gene content data. PANINI is available at and code at
Subject: pangenome
microbial population genomics
machine learning
web application
111 Mathematics
318 Medical biotechnology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion

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