Title
Trans-national Infrastructure for Plant Genomic Science

CoPED ID
02501e3e-92d3-4c7d-8982-a9c87b350f0c

Status
Closed

Funder

Value
£280,706

Start Date
Aug. 31, 2011

End Date
Aug. 30, 2015

Description

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Food and energy security are major challenges facing humanity in the coming decades. The falling costs of nucleotide sequencing are opening up significant opportunities for crop improvement through plant breeding and increased understanding of plant biology; in particular through interpreting the growing volume of plant genomics data in the context of phenotype. However, at present, there is no adequate infrastructure for plant genomic data. TransPLANT will develop a new infrastructure for this data, leveraging the experience of medical informatics while addressing the particular challenges and opportunities of plant genomics.

TGAC will lead the work package on the implementation of resource-intensive algorithms for plant genomics data. This will include the evaluation of current resource-intensive algorithms for plants genomics data; building a network of developers with expertise in algorithms for plant genomics; and the implementation of novel algorithmic solutions for concrete challenges in large plant genomes. One focus will be on the evaluation and development of strategies for plant genome sequencing and assembly. The aim being to develop guidelines for genome sequencing and assembly strategies taking into account the characteristics of the genome in question, including the presence of repeats, heterozygosity and polyploidy. Other tasks include the evaluation and development of data structures for algorithm optimisation; testing methods, tools and pipelines for gene and repeat annotation; and development of tools for the enablement of virtual plant breeding.

Mario Caccamo PI_PER
David Swarbreck COI_PER
Sarah Dyer COI_PER

Subjects by relevance
  1. Genomics
  2. Genome
  3. Genes
  4. Plants
  5. Plant breeding
  6. Algorithms
  7. Bioinformatics

Extracted key phrases
  1. Plant genomic datum
  2. Plant genome sequencing
  3. Large plant genome
  4. Plant Genomic Science
  5. Virtual plant breeding
  6. Plant biology
  7. National Infrastructure
  8. Trans
  9. Energy security
  10. Major challenge
  11. Datum structure
  12. Particular challenge
  13. Intensive algorithm
  14. Food
  15. Concrete challenge

Related Pages

UKRI project entry

UK Project Locations