Coinfinder: detecting significant associations and dissociations in pangenomes
Year: 2020
Type: article
Abstract: 2. Abstract The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whether sets of homologous genes (gene families) in pangenomes associate or dissociate with each other (i.e. are “coincident”) more often than would be expected by chance. Coinfinder employs a user-supplied phylogenetic tree in order to assess the lineage-dependence (i.e. the phylogenetic distribution) of each accessory gene, allowing Coinfinder to focus on coincident gene pairs whose joint presence is not simply because they happened to appear in the same clade, but rather that they tend to appear together more often than expected across the phylogeny. Coinfinder is implemented in C++, Python3, and R and is freely available under the GPU license from https://github.com/fwhelan/coinfinder . 3. Impact statement Coinfinder identifies genes that co-occur (associate) or avoid (dissociate) with each other across the accessory genomes of a pangenome of interest. Genes that associate or dissociate more often than expected by chance, suggests that those genes have a connection (attraction or repulsion) that is interesting to explore. Identification of these groups of genes will further the field’s understanding of the importance of accessory genes. Coinfinder is a freely available, open-source software which can identify gene patterns locally on a personal computer in a matter of hours. 4. Data summary Coinfinder is freely available at https://github.com/fwhelan/coinfinder . A list of the Identifiers of the genomes used within as well as all input/output files are available at https://github.com/fwhelan/coinfinder-manuscript . The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Source: Microbial Genomics
Institutions: University of Nottingham, University of Manchester
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,839
Awards: Investigating how non-homologous recombination structures genes, proteins, operons, clusters, genomes and ecosystems, Investigating how non-homologous recombination structures genes, proteins, operons, clusters, genomes and ecosystems, Concepts of Graph Theory Applied to the Human Microbiome
OpenAlex ID: W3008753509