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Online resources

The Plant Bioinformatics Group has developed a number of online data resources built to underpin both internal and external projects.

All of our current systems are implemented using the same common LAMP (Linux, Apache, MySQL and Perl) platform. Our latest web-based databases all are built using the Germinate platform which takes the common LAMP system and adds common components specific to genotyping and phenotyping experiments which can be reused as required. The use of the standard system allows us to rapidly develop new applications and resources to support the scientific work being carried out at the Institute.

The scale of our data resources range from relatively small datasets involving hundreds of entries such as the Plant snoRNA Database to the systems utilised in large scale genotyping experiments built on the Germinate platform which deal with many millions of datapoints.

Germinate
Germinate logoGerminate is a generic plant data management platform implemented in MySQL and is designed to act as a scaffolding on which complex web-based applications can be developed to leverage information from experimentally derived data. Germinate currently handles phenotypic, genotypic and passport data.

 

AtNoPDB
Screenshot of AtNoPDB databaseThe Arabidopsis Nucleolar Protein database provides information on plant proteins in comparison to human and yeast proteins and images of cellular localisations for over a third of these proteins. This data was derived from a proteomic analysis of nucleoli purified from Arabidopsis cell cultures.

Barley SNP Database
Screenshot of Barley SNP databaseThe Barley SNP Database contains information on SNP polymorphisms from genes associated with abiotic stress in eight cultivars of barley. This online resource offers the user various visualizations that show these polymorphisms within the context of the aligned genes from the eight cultivars, as well as primers used to map these polymorphic markers and background about the gene sequences. This detailed dataset was the result of a SNP discovery pipeline which uses phred, phrap, consed and polyphred to discover, view and annotate polymorphic sites.

ProtLocDB
ProtLocDB is a protein localisation database that contains sequence information, BLAST results and the subcellular localisations of numerous partial plant cDNA-GFP fusions expressed from a Tobacco Mosaic Virus vector. Images can be searched by localization within the cell, by AGI number or by sequence descriptions.

Plant snoRNA Database
Screenshot of Plant snoRNA databaseThe Plant snoRNA Database and website brings together information from three independent computer-assisted searches of the Arabidopsis genome for box C/D snoRNA genes and from studies of ncRNAs. To date, the Arabidopsis box C/D snoRNAs have been used to identify approximately 250 genes from different non-Arabidopsis plant species and these sequences are included as alignments in the Database. The Database also provides a unifying nomenclature for all of the plant snoRNA genes.

Wheat inSitu Database
The Wheat In Situ Database resource was developed wth the John Innes Centre and Syngenta and provides a gateway to the information obtained from a high-throughput wheat in situ hybridization project funded by BBSRC and Syngenta. mRNA in situ hybridisation was used to determine the spatial experssion pattern of genes expressed in the developing wheat caryopsis.

Research

Areas of Interest


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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.