Award details

A computational cloud framework for the study of gene families

Reference	BBS/E/T/000GP092
Principal Investigator / Supervisor	Professor Anthony Hall
Co-Investigators / Co-Supervisors
Institution	Earlham Institute
Department	Earlham Institute Department
Funding type	Research
Value (£)	8,206
Status	Completed
Type	Institute Project
Start date	01/03/2017
End date	31/03/2017
Duration	0 months

Abstract

Genomics is moving from studying single reference genomes to study of multiple genomes from same species, allowing us to uncover the pan-genome. The pan-genome or supra-genome describes a core set of genes common in all strains, and a non-core set that is found in only a sub-set or single strain. Commonly this is seen as an expansion of an existing gene family. Study of these gene families is important for various reasons, as each gene family can be understood in terms of its function and its evolution across strains. As an example, NB-LRR genes or resistance genes in plants are responsible for disease resistance and show expansion and contraction across accessions. Critically, new R-genes have the potential of being important targets for plant breeders. As the field is moving towards the study of pan-genomes using next generation sequencing techniques, there is a timely need for appropriate software for data analysis. Given the large size of datasets, it is preferable that the software runs on community accessible cloud resources. We propose to build an open-source, cloud enabled, software toolkit to analyze gene-family datasets. We propose to use BBSRC funded iPlant-UK compute infrastructure as the cloud platform of choice. iPlant-UK is maintained by a dedicated team of experts and offers large compute resources with easy to use graphical interfaces for bioinformaticians and bench-biologists. Further, we plan to use the software for two case-studies - 1) Extract the pan-NB-LRRome for bread wheat and 2) for study of gene families in Tsetse fly in context of their role as disease vectors.

Summary

unavailable

Committee	Not funded via Committee
Research Topics	Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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