The SCRI Plant Bioinformatics Group has developed a number of on-line 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 by the Genetics programme here at SCRI.

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.

AtNoPDB

The 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.

Reference: Brown, J.W., Shaw, P.J., Shaw, P., Marshall, D.F. Arabidopsis nucleolar protein database (AtNoPDB). Nucleic Acids Research. 2005 Jan 1;33(Database issue):D633-6.

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

The 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.

Reference: Brown, J.W., Echeverria, M., Qu, L.H., Lowe, T.M., Bachellerie, J.P., Hüttenhofer, A., Kastenmayer, J.P., Green, P.J., Shaw, P., Marshall, D.F. Plant snoRNA database. Nucleic Acids Research 2003 Jan 1;31(1), 432-5.

Barley SNP Database

The 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.

Wheat In Situ 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.

For further information on the work that the Plant Bioinformatics Group carries out and to get more information on any of our online databases please visit the Bioinformatics website or contact us at bioinf@scri.ac.uk.