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Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes.
- Source :
-
Genes . Jul2019, Vol. 10 Issue 7, p521-521. 1p. - Publication Year :
- 2019
-
Abstract
- Although the pan-genome concept originated in prokaryote genomics, an increasing number of eukaryote species pan-genomes have also been analysed. However, there is a relative lack of software intended for eukaryote pan-genome analysis compared to that available for prokaryotes. In a previous study, we analysed the pan-genomes of four model fungi with a computational pipeline that constructed pan-genomes using the synteny-dependent Pan-genome Ortholog Clustering Tool (PanOCT) approach. Here, we present a modified and improved version of that pipeline which we have called Pangloss. Pangloss can perform gene prediction for a set of genomes from a given species that the user provides, constructs and optionally refines a species pan-genome from that set using PanOCT, and can perform various functional characterisation and visualisation analyses of species pan-genome data. To demonstrate Pangloss's capabilities, we constructed and analysed a species pan-genome for the oleaginous yeast Yarrowia lipolytica and also reconstructed a previously-published species pan-genome for the opportunistic respiratory pathogen Aspergillus fumigatus. Pangloss is implemented in Python, Perl and R and is freely available under an open source GPLv3 licence via GitHub. [ABSTRACT FROM AUTHOR]
- Subjects :
- *EUKARYOTES
*ASPERGILLUS fumigatus
*NUMBERS of species
*SPECIES
Subjects
Details
- Language :
- English
- ISSN :
- 20734425
- Volume :
- 10
- Issue :
- 7
- Database :
- Academic Search Index
- Journal :
- Genes
- Publication Type :
- Academic Journal
- Accession number :
- 137798630
- Full Text :
- https://doi.org/10.3390/genes10070521